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Gene Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro (GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro samples were split into upregulated and downregulated genes (up/down) and the analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults for the differential gene expression analysis for samples from adult mice before (HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively). Each sheet shows the results for a different comparison. Sheets 1-3 show results for comparisons between timepoints for wild type (WT) samples only and sheets 4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results for comparisons between genotypes at each time point and sheet 10 contains the results for the analysis of differential expression trajectories between wild type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults for k-means clustering of genes by expression. Sheet 1 shows clustering of just the genes with significantly different expression trajectories between genotypes. Sheet 2 shows clustering of all genes that are significantly differentially expressed in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment analysis and EWCE analysis for enrichment of cell type specific genes for each cluster identified by clustering genes with different expression trajectories (see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet 1 shows protein protein interaction data generated from these results (combined with data from the STRING database. Sheet 2 shows the results of the statistical analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows results for differential binding of PolII at the transcription start site (TSS) between genotypes and sheets 2+3 show the corresponding GO enrichment analysis for these differentially bound genes. 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The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. "}],"month":"03","oa":1,"publisher":"Institute of Science and Technology Austria"},{"department":[{"_id":"BeVi"}],"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)","file_date_updated":"2020-07-14T12:47:08Z","article_processing_charge":"No","author":[{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, 10.15479/AT:ISTA:109.","chicago":"Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:109.","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","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.","mla":"Vicoso, Beatriz. Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018). Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:109."},"date_updated":"2024-02-21T13:45:12Z","keyword":["schistosoma","Z-chromosome","gene expression"],"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"}],"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","_id":"5586","date_created":"2018-12-12T12:31:40Z","contributor":[{"orcid":"0000-0002-8101-2518","last_name":"Picard","first_name":"Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2018-07-24T00:00:00Z","related_material":{"record":[{"id":"131","status":"public","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:109","day":"24","file":[{"creator":"system","date_updated":"2020-07-14T12:47:08Z","file_size":11918144,"date_created":"2018-12-12T13:02:35Z","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5601","checksum":"e60b484bd6f55c08eb66a189cb72c923"}],"year":"2018","datarep_id":"109","has_accepted_license":"1","month":"07","oa":1,"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)."}]},{"status":"public","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":"5583","title":"Data and Python scripts supporting Python package FAPS","file_date_updated":"2020-07-14T12:47:07Z","department":[{"_id":"NiBa"}],"author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","last_name":"Ellis"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95.","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.","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","short":"T. Ellis, (2018).","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95","mla":"Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95."},"date_updated":"2024-02-21T13:45:01Z","month":"02","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}],"date_published":"2018-02-12T00:00:00Z","related_material":{"record":[{"status":"public","id":"286","relation":"research_paper"}]},"doi":"10.15479/AT:ISTA:95","contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-12T12:31:39Z","file":[{"date_updated":"2020-07-14T12:47:07Z","file_size":122048,"creator":"system","date_created":"2018-12-12T13:02:41Z","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","content_type":"text/csv","access_level":"open_access","relation":"main_file","file_id":"5606","checksum":"fc6aab51439f2622ba6df8632e66fd4f"},{"file_size":235980,"date_updated":"2020-07-14T12:47:07Z","creator":"system","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","date_created":"2018-12-12T13:02:42Z","content_type":"text/csv","relation":"main_file","access_level":"open_access","checksum":"92347586ae4f8a6eb7c04354797bf314","file_id":"5607"},{"content_type":"text/csv","access_level":"open_access","relation":"main_file","file_id":"5608","checksum":"3300813645a54e6c5c39f41917228354","date_updated":"2020-07-14T12:47:07Z","file_size":311712,"creator":"system","date_created":"2018-12-12T13:02:43Z","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv"},{"relation":"main_file","access_level":"open_access","content_type":"application/zip","checksum":"e739fc473567fd8f39438b445fc46147","file_id":"5609","creator":"system","file_size":342090,"date_updated":"2020-07-14T12:47:07Z","file_name":"IST-2018-95-v1+4_faps_scripts.zip","date_created":"2018-12-12T13:02:44Z"}],"day":"12","has_accepted_license":"1","year":"2018","datarep_id":"95"},{"_id":"5569","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","keyword":["microscopy","microfluidics"],"citation":{"mla":"Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","short":"T. Bergmiller, N. Nikolic, (2018).","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","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.","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, 10.15479/AT:ISTA:74."},"date_updated":"2024-02-21T13:44:45Z","ddc":["579"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7385","author":[{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"last_name":"Nikolic","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:04Z","title":"Time-lapse microscopy data","abstract":[{"lang":"eng","text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic."}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","has_accepted_license":"1","datarep_id":"74","year":"2018","file":[{"date_created":"2018-12-12T13:04:39Z","file_name":"IST-2018-74-v1+2_15-11-05.zip","creator":"system","date_updated":"2020-07-14T12:47:04Z","file_size":3558703796,"checksum":"61ebb92213cfffeba3ddbaff984b81af","file_id":"5637","access_level":"open_access","relation":"main_file","content_type":"application/zip"},{"date_updated":"2020-07-14T12:47:04Z","file_size":1830422606,"creator":"system","date_created":"2018-12-12T13:04:55Z","file_name":"IST-2018-74-v1+3_15-07-31.zip","content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"bf26649af310ef6892d68576515cde6d","file_id":"5638"},{"relation":"main_file","access_level":"open_access","content_type":"application/zip","file_id":"5639","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","creator":"system","file_size":2140849248,"date_updated":"2020-07-14T12:47:04Z","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","date_created":"2018-12-12T13:05:11Z"}],"day":"07","related_material":{"record":[{"relation":"research_paper","status":"public","id":"438"}]},"doi":"10.15479/AT:ISTA:74","date_published":"2018-02-07T00:00:00Z","date_created":"2018-12-12T12:31:35Z"},{"year":"2018","datarep_id":"111","has_accepted_license":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","file_id":"5641","checksum":"97992e3e8cf8544ec985a48971708726","creator":"system","file_size":14376,"date_updated":"2020-07-14T12:47:08Z","file_name":"IST-2018-111-v1+1_CODES.zip","date_created":"2018-12-12T13:05:13Z"}],"day":"21","ec_funded":1,"date_created":"2018-12-12T12:31:41Z","doi":"10.15479/AT:ISTA:62","date_published":"2018-09-21T00:00:00Z","related_material":{"record":[{"relation":"research_paper","id":"161","status":"public"}]},"abstract":[{"lang":"eng","text":"Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015)."}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"09","citation":{"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.","ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 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","mla":"De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.","ista":"De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:62.","chicago":"De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:62."},"date_updated":"2024-02-21T13:45:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"article_processing_charge":"No","author":[{"last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","file_date_updated":"2020-07-14T12:47:08Z","department":[{"_id":"GaTk"}],"_id":"5587","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"],"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"status":"public"},{"author":[{"last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"}],"article_processing_charge":"No","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:11Z","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","citation":{"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","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."},"date_updated":"2024-02-21T13:59:18Z","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","status":"public","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"_id":"5757","related_material":{"record":[{"status":"public","id":"6089","relation":"research_paper"}]},"date_published":"2018-12-19T00:00:00Z","doi":"10.15479/at:ista:/5757","date_created":"2018-12-19T14:22:35Z","ec_funded":1,"contributor":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"},{"last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"has_accepted_license":"1","year":"2018","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","file_id":"5758","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","creator":"cfraisse","file_size":369837892,"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS1.zip","date_created":"2018-12-19T14:19:52Z"},{"date_created":"2018-12-19T14:19:49Z","file_name":"FileS2.zip","date_updated":"2020-07-14T12:47:11Z","file_size":84856909,"creator":"cfraisse","checksum":"3592e467b4d8206650860b612d6e12f3","file_id":"5759","content_type":"application/zip","access_level":"open_access","relation":"main_file"},{"file_id":"5760","checksum":"c37ac5d5437c457338afc128c1240655","relation":"main_file","access_level":"open_access","content_type":"text/plain","file_name":"FileS3.txt","date_created":"2018-12-19T14:19:49Z","creator":"cfraisse","file_size":881133,"date_updated":"2020-07-14T12:47:11Z"},{"relation":"main_file","access_level":"open_access","content_type":"text/plain","checksum":"943dfd14da61817441e33e3e3cb8cdb9","file_id":"5761","creator":"cfraisse","file_size":883742,"date_updated":"2020-07-14T12:47:11Z","file_name":"FileS4.txt","date_created":"2018-12-19T14:19:49Z"},{"file_id":"5762","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","access_level":"open_access","relation":"main_file","content_type":"text/plain","date_created":"2018-12-19T14:19:49Z","file_name":"FileS5.txt","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":2495437},{"creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":15913457,"date_created":"2018-12-19T14:19:50Z","file_name":"FileS6.txt","access_level":"open_access","relation":"main_file","content_type":"text/plain","file_id":"5763","checksum":"f40f661b987ca6fb6b47f650cbbb04e6"},{"creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","file_size":2584120,"date_created":"2018-12-19T14:19:50Z","file_name":"FileS7.txt","access_level":"open_access","relation":"main_file","content_type":"text/plain","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","file_id":"5764"},{"date_created":"2018-12-19T14:19:50Z","file_name":"FileS8.txt","date_updated":"2020-07-14T12:47:11Z","file_size":2446059,"creator":"cfraisse","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","file_id":"5765","content_type":"text/plain","access_level":"open_access","relation":"main_file"},{"file_name":"FileS9.txt","date_created":"2018-12-19T14:19:50Z","file_size":100737,"date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","file_id":"5766","content_type":"text/plain","relation":"main_file","access_level":"open_access"}],"day":"19","publisher":"Institute of Science and Technology Austria","oa":1,"month":"12","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"},{"day":"20","file":[{"file_size":16507,"date_updated":"2020-07-14T12:47:07Z","creator":"system","file_name":"IST-2018-108-v1+1_data_figures.xlsx","date_created":"2018-12-12T13:02:45Z","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","relation":"main_file","access_level":"open_access","checksum":"1435781526c77413802adee0d4583cce","file_id":"5611"}],"year":"2018","datarep_id":"108","has_accepted_license":"1","ec_funded":1,"date_created":"2018-12-12T12:31:40Z","date_published":"2018-07-20T00:00:00Z","doi":"10.15479/AT:ISTA:108","related_material":{"record":[{"relation":"research_paper","id":"67","status":"public"},{"status":"public","id":"6371","relation":"research_paper"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Mean repression values and standard error of the mean are given for all operator mutant libraries."}],"month":"07","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-03-27T23:30:48Z","citation":{"ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, 10.15479/AT:ISTA:108.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:108.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:10.15479/AT:ISTA:108","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:108","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","ieee":"C. Igler, M. 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It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408."}],"title":"Multi-electrode array recording from salamander retinal ganglion cells","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:03Z","article_processing_charge":"No","author":[{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"last_name":"Amodei","full_name":"Amodei, Dario","first_name":"Dario"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"},{"full_name":"Berry, Michael","last_name":"Berry","first_name":"Michael"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"ista":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode array recording from salamander retinal ganglion cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:61.","chicago":"Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:61.","ama":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode array recording from salamander retinal ganglion cells. 2017. doi:10.15479/AT:ISTA:61","apa":"Marre, O., Tkačik, G., Amodei, D., Schneidman, E., Bialek, W., & Berry, M. (2017). Multi-electrode array recording from salamander retinal ganglion cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:61","short":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017).","ieee":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. 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Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in \"Feature Correspondence via Graph Matching: Models and Global Optimization.\" by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. ","lang":"eng"}],"oa_version":"Published Version","acknowledgement":"We thank Vladimir Kolmogorov and Stephan Saalfeld forinspiring discussions.","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","has_accepted_license":"1","year":"2017","datarep_id":"57","day":"13","file":[{"date_created":"2018-12-12T13:02:54Z","file_name":"IST-2017-57-v1+1_wormMatchingProblems.zip","creator":"system","date_updated":"2020-07-14T12:47:03Z","file_size":327042819,"checksum":"3dc3e1306a66028a34181ebef2923139","file_id":"5614","access_level":"open_access","relation":"main_file","content_type":"application/zip"}],"date_published":"2017-02-13T00:00:00Z","doi":"10.15479/AT:ISTA:57","date_created":"2018-12-12T12:31:32Z","_id":"5561","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":["graph matching","feature matching","QAP","MAP-inference"],"citation":{"ista":"Kainmueller D, Jug F, Rother C, Meyers G. 2017. 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(2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions"}],"oa_version":"Published Version","doi":"10.15479/AT:ISTA:64","date_published":"2017-03-20T00:00:00Z","date_created":"2018-12-12T12:31:33Z","has_accepted_license":"1","year":"2017","datarep_id":"64","day":"20","file":[{"file_name":"IST-2016-45-v1+1_PaperCode.zip","date_created":"2018-12-12T13:02:37Z","file_size":296722548,"date_updated":"2020-07-14T12:47:03Z","creator":"system","file_id":"5602","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","content_type":"application/zip","relation":"main_file","access_level":"open_access"}],"type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"status":"public","_id":"5563","author":[{"last_name":"Lukacisin","orcid":"0000-0001-6549-4177","full_name":"Lukacisin, Martin","first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:03Z","department":[{"_id":"ToBo"}],"title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","citation":{"mla":"Lukacisin, Martin. 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We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)","lang":"eng"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:29Z","doi":"10.15479/AT:ISTA:34","date_published":"2016-02-19T00:00:00Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1382"}]},"year":"2016","datarep_id":"34","has_accepted_license":"1","day":"19","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/zip","checksum":"950f85b80427d357bfeff09608ba02e9","file_id":"5594","creator":"system","file_size":4468543,"date_updated":"2020-07-14T12:47:00Z","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","date_created":"2018-12-12T13:02:27Z"}],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","status":"public","_id":"5550","article_processing_charge":"No","publist_id":"5828","author":[{"last_name":"Ellis","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"}],"department":[{"_id":"NiBa"}],"title":"Flower colour data and phylogeny (NEXUS) files","file_date_updated":"2020-07-14T12:47:00Z","date_updated":"2024-02-21T13:49:54Z","citation":{"mla":"Ellis, Thomas, and David Field. 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Synthetic discrete tomography problems, Institute of Science and Technology Austria, 10.15479/AT:ISTA:46.","chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:46.","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016.","short":"P. Swoboda, (2016).","apa":"Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:46","ama":"Swoboda P. Synthetic discrete tomography problems. 2016. doi:10.15479/AT:ISTA:46","mla":"Swoboda, Paul. Synthetic Discrete Tomography Problems. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:46."},"file_date_updated":"2020-07-14T12:47:02Z","title":"Synthetic discrete tomography problems","department":[{"_id":"VlKo"}],"author":[{"last_name":"Swoboda","full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul"}],"article_processing_charge":"No","_id":"5557","status":"public","keyword":["discrete tomography"],"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)"}},{"has_accepted_license":"1","datarep_id":"37","year":"2016","file":[{"creator":"system","date_updated":"2020-07-14T12:47:01Z","file_size":132808,"date_created":"2018-12-12T13:03:02Z","file_name":"IST-2016-37-v1+1_paternity_archive.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5620","checksum":"4ae751b1fa4897fa216241f975a57313"}],"day":"19","doi":"10.15479/AT:ISTA:37","date_published":"2016-02-19T00:00:00Z","related_material":{"record":[{"relation":"research_paper","id":"1398","status":"public"}]},"date_created":"2018-12-12T12:31:30Z","contributor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_manager","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"abstract":[{"text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org.","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","citation":{"ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, 10.15479/AT:ISTA:37.","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:37.","apa":"Field, D., & Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:37","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37","short":"D. Field, T. Ellis, (2016).","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","mla":"Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:37."},"date_updated":"2024-02-21T13:51:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"author":[{"full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:01Z","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","_id":"5553","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":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"]},{"_id":"5551","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data","status":"public","date_updated":"2024-02-21T13:51:27Z","citation":{"mla":"Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","short":"T. Ellis, (2016).","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35.","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:35."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"file_date_updated":"2020-07-14T12:47:01Z","department":[{"_id":"NiBa"}],"title":"Data on pollinator observations and offpsring phenotypes","abstract":[{"text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.","lang":"eng"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"02","year":"2016","datarep_id":"35","has_accepted_license":"1","file":[{"creator":"system","date_updated":"2020-07-14T12:47:01Z","file_size":32775,"date_created":"2018-12-12T13:05:12Z","file_name":"IST-2016-35-v1+1_array_data.zip","access_level":"open_access","relation":"main_file","content_type":"application/zip","file_id":"5640","checksum":"aa3eb85d52b110cd192aa23147c4d4f3"}],"day":"19","date_created":"2018-12-12T12:31:29Z","contributor":[{"last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"doi":"10.15479/AT:ISTA:35","date_published":"2016-02-19T00:00:00Z","related_material":{"record":[{"status":"public","id":"1398","relation":"research_paper"}]}},{"date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:36","related_material":{"record":[{"relation":"research_paper","id":"1398","status":"public"}]},"contributor":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"date_created":"2018-12-12T12:31:30Z","has_accepted_license":"1","datarep_id":"36","year":"2016","file":[{"creator":"system","file_size":44905,"date_updated":"2020-07-14T12:47:01Z","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","date_created":"2018-12-12T13:03:07Z","relation":"main_file","access_level":"open_access","content_type":"application/zip","checksum":"cbc61b523d4d475a04a737d50dc470ef","file_id":"5625"}],"day":"19","publisher":"Institute of Science and Technology Austria","oa":1,"month":"02","abstract":[{"lang":"eng","text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation."}],"oa_version":"Published Version","author":[{"first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254"}],"article_processing_charge":"No","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:01Z","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","date_updated":"2024-02-21T13:51:40Z","citation":{"chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:36.","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, 10.15479/AT:ISTA:36.","mla":"Ellis, Thomas. Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:36.","short":"T. Ellis, (2016).","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:36"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","status":"public","_id":"5552"},{"datarep_id":"43","year":"2016","has_accepted_license":"1","day":"12","file":[{"content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","file_id":"5626","date_updated":"2020-07-14T12:47:01Z","file_size":1123495,"creator":"system","date_created":"2018-12-12T13:03:08Z","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip"}],"contributor":[{"last_name":"Steinrück","contributor_type":"researcher","first_name":"Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"researcher","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","first_name":"Fabienne","last_name":"Jesse"}],"date_created":"2018-12-12T12:31:30Z","doi":"10.15479/AT:ISTA:43","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1131"}]},"date_published":"2016-05-12T00:00:00Z","abstract":[{"text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution.","lang":"eng"}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","month":"05","date_updated":"2024-02-21T13:50:34Z","citation":{"chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:43.","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, 10.15479/AT:ISTA:43.","mla":"Tugrul, Murat. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:43.","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:43","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:10.15479/AT:ISTA:43","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","short":"M. Tugrul, (2016)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758"}],"title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"file_date_updated":"2020-07-14T12:47:01Z","_id":"5554","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":["RNAP binding","de novo promoter evolution","lac promoter"],"status":"public"},{"doi":"10.15479/AT:ISTA:48","date_published":"2016-09-23T00:00:00Z","related_material":{"record":[{"relation":"other","status":"public","id":"1122"}]},"date_created":"2018-12-12T12:31:31Z","file":[{"file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2","date_created":"2018-12-12T13:02:18Z","file_size":55237885,"date_updated":"2020-07-14T12:47:02Z","creator":"system","checksum":"5b1b256ad796fbddb4b7729f5e45e444","file_id":"5589","content_type":"application/x-bzip2","relation":"main_file","access_level":"open_access"}],"day":"23","has_accepted_license":"1","year":"2016","datarep_id":"48","month":"09","publisher":"Institute of Science and Technology Austria","oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"PhD thesis LaTeX source code"}],"file_date_updated":"2020-07-14T12:47:02Z","department":[{"_id":"ChWo"}],"title":"Tracking, Correcting and Absorbing Water Surface Waves","author":[{"last_name":"Bojsen-Hansen","orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten","first_name":"Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6238","article_processing_charge":"No","ddc":["004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:50:48Z","citation":{"mla":"Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:48.","ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:10.15479/AT:ISTA:48","apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:48","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016.","short":"M. Bojsen-Hansen, (2016).","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:48.","ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 10.15479/AT:ISTA:48."},"status":"public","pubrep_id":"640","type":"research_data","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)"},"_id":"5558"},{"has_accepted_license":"1","year":"2016","datarep_id":"45","day":"25","file":[{"checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","file_id":"5616","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_name":"IST-2016-45-v1+1_PaperCode.zip","date_created":"2018-12-12T13:02:58Z","file_size":296722548,"date_updated":"2020-07-14T12:47:02Z","creator":"system"}],"doi":"10.15479/AT:ISTA:45","related_material":{"record":[{"relation":"used_in_publication","status":"deleted","id":"8431"},{"status":"public","id":"1029","relation":"research_paper"}]},"date_published":"2016-08-25T00:00:00Z","date_created":"2018-12-12T12:31:31Z","abstract":[{"text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"08","citation":{"chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:45.","ista":"Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:45.","mla":"Lukacisin, Martin, et al. MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:45.","ama":"Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2016. doi:10.15479/AT:ISTA:45","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2016). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:45","short":"M. Lukacisin, M. Landon, R. Jajoo, (2016).","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016."},"date_updated":"2024-02-21T13:51:53Z","ddc":["571"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Lukacisin","orcid":"0000-0001-6549-4177","full_name":"Lukacisin, Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Matthieu","full_name":"Landon, Matthieu","last_name":"Landon"},{"last_name":"Jajoo","full_name":"Jajoo, Rishi","first_name":"Rishi"}],"article_processing_charge":"No","title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:47:02Z","_id":"5556","type":"research_data","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"status":"public","keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"]},{"oa":1,"publisher":"Institute of Science and Technology Austria","date_created":"2018-12-12T12:31:29Z","date_published":"2015-08-13T00:00:00Z","doi":"10.15479/AT:ISTA:28","day":"13","year":"2015","has_accepted_license":"1","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"title":"Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes","article_processing_charge":"No","author":[{"first_name":"Andreas","id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","full_name":"Fellner, Andreas","last_name":"Fellner"}],"publist_id":"5564","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Fellner, Andreas. Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria, 2015, doi:10.15479/AT:ISTA:28.","apa":"Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:28","ama":"Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. 2015. doi:10.15479/AT:ISTA:28","ieee":"A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015.","short":"A. Fellner, (2015).","chicago":"Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015. https://doi.org/10.15479/AT:ISTA:28.","ista":"Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:28."},"month":"08","oa_version":"Published Version","abstract":[{"text":"This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees.\r\nThe archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library.\r\nTo execute the program, please have a look at the README.txt, which provides instructions and further information on the archive.\r\nThe archive contains scripts that (if run often enough) reproduces the data presented in the publication.","lang":"eng"}],"contributor":[{"last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"ec_funded":1,"related_material":{"record":[{"id":"1603","status":"public","relation":"popular_science"}]},"file":[{"file_size":49557109,"date_updated":"2020-07-14T12:47:00Z","creator":"system","file_name":"IST-2015-28-v1+2_Fellner_DataRep.zip","date_created":"2018-12-12T13:02:31Z","content_type":"application/zip","relation":"main_file","access_level":"open_access","file_id":"5597","checksum":"b8bcb43c0893023cda66c1b69c16ac62"}],"datarep_id":"28","keyword":["Markov Decision Process","Decision Tree","Probabilistic Verification","Counterexample Explanation"],"status":"public","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","_id":"5549","file_date_updated":"2020-07-14T12:47:00Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ddc":["004"],"date_updated":"2024-02-21T13:52:07Z"}]