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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.","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_published":"2018-07-24T00:00:00Z","type":"research_data","datarep_id":"109","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)."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5586","status":"public","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)","ddc":["570"],"file":[{"date_updated":"2020-07-14T12:47:08Z","date_created":"2018-12-12T13:02:35Z","checksum":"e60b484bd6f55c08eb66a189cb72c923","file_id":"5601","relation":"main_file","creator":"system","content_type":"application/zip","file_size":11918144,"file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","access_level":"open_access"}],"oa_version":"Published Version"},{"article_processing_charge":"No","has_accepted_license":"1","day":"12","month":"02","doi":"10.15479/AT:ISTA:95","date_published":"2018-02-12T00:00:00Z","oa":1,"tmp":{"short":"CC0 (1.0)","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)"},"citation":{"ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","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","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95.","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi: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.","short":"T. Ellis, (2018).","mla":"Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95."},"abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:07Z","type":"research_data","datarep_id":"95","related_material":{"record":[{"relation":"research_paper","status":"public","id":"286"}]},"contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"author":[{"full_name":"Ellis, Thomas","first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"}],"file":[{"file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","access_level":"open_access","content_type":"text/csv","file_size":122048,"creator":"system","relation":"main_file","file_id":"5606","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:41Z","checksum":"fc6aab51439f2622ba6df8632e66fd4f"},{"creator":"system","content_type":"text/csv","file_size":235980,"access_level":"open_access","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","checksum":"92347586ae4f8a6eb7c04354797bf314","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:42Z","file_id":"5607","relation":"main_file"},{"file_id":"5608","relation":"main_file","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:43Z","checksum":"3300813645a54e6c5c39f41917228354","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","access_level":"open_access","creator":"system","content_type":"text/csv","file_size":311712},{"content_type":"application/zip","file_size":342090,"creator":"system","access_level":"open_access","file_name":"IST-2018-95-v1+4_faps_scripts.zip","checksum":"e739fc473567fd8f39438b445fc46147","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:44Z","relation":"main_file","file_id":"5609"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:45:01Z","date_created":"2018-12-12T12:31:39Z","_id":"5583","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"status":"public","title":"Data and Python scripts supporting Python package FAPS"},{"keyword":["microscopy","microfluidics"],"article_processing_charge":"No","has_accepted_license":"1","month":"02","day":"07","citation":{"mla":"Bergmiller, Tobias, and Nela Nikolic. Time-Lapse Microscopy Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:74.","short":"T. Bergmiller, N. Nikolic, (2018).","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.","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 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.","apa":"Bergmiller, T., & Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:74","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018."},"tmp":{"short":"CC0 (1.0)","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)"},"oa":1,"doi":"10.15479/AT:ISTA:74","date_published":"2018-02-07T00:00:00Z","type":"research_data","datarep_id":"74","publist_id":"7385","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"}],"file_date_updated":"2020-07-14T12:47:04Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"}],"title":"Time-lapse microscopy data","status":"public","ddc":["579"],"_id":"5569","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"IST-2018-74-v1+2_15-11-05.zip","access_level":"open_access","file_size":3558703796,"content_type":"application/zip","creator":"system","relation":"main_file","file_id":"5637","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:04:39Z","checksum":"61ebb92213cfffeba3ddbaff984b81af"},{"creator":"system","file_size":1830422606,"content_type":"application/zip","access_level":"open_access","file_name":"IST-2018-74-v1+3_15-07-31.zip","checksum":"bf26649af310ef6892d68576515cde6d","date_created":"2018-12-12T13:04:55Z","date_updated":"2020-07-14T12:47:04Z","file_id":"5638","relation":"main_file"},{"creator":"system","content_type":"application/zip","file_size":2140849248,"file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","access_level":"open_access","date_created":"2018-12-12T13:05:11Z","date_updated":"2020-07-14T12:47:04Z","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","file_id":"5639","relation":"main_file"}],"date_updated":"2024-02-21T13:44:45Z","date_created":"2018-12-12T12:31:35Z","related_material":{"record":[{"id":"438","relation":"research_paper","status":"public"}]},"author":[{"full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela"}]},{"date_published":"2018-07-30T00:00:00Z","citation":{"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.","short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","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.","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","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.","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.","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"},"publication":"Nature Communications","article_processing_charge":"No","has_accepted_license":"1","day":"30","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2018_NatureComm_DeMartino.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1043205,"file_id":"5728","relation":"main_file","date_created":"2018-12-17T16:44:28Z","date_updated":"2020-07-14T12:45:06Z","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"161","intvolume":" 9","title":"Statistical mechanics for metabolic networks during steady state growth","status":"public","ddc":["570"],"issue":"1","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."}],"type":"journal_article","doi":"10.1038/s41467-018-05417-9","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000440149300021"]},"project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"quality_controlled":"1","month":"07","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5587"}]},"author":[{"full_name":"De Martino, Daniele","first_name":"Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706"},{"last_name":"Mc","first_name":"Andersson Anna","full_name":"Mc, Andersson Anna"},{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"}],"volume":9,"date_updated":"2024-02-21T13:45:39Z","date_created":"2018-12-11T11:44:57Z","year":"2018","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"publisher":"Springer Nature","publication_status":"published","ec_funded":1,"publist_id":"7760","file_date_updated":"2020-07-14T12:45:06Z","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"2988"},{"doi":"10.15479/AT:ISTA:62","date_published":"2018-09-21T00:00:00Z","citation":{"short":"D. De Martino, G. Tkačik, (2018).","mla":"De Martino, Daniele, and Gašper Tkačik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:62.","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.","ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62","ieee":"D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.","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","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."},"tmp":{"short":"CC0 (1.0)","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)"},"oa":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","article_processing_charge":"No","day":"21","month":"09","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"related_material":{"record":[{"id":"161","status":"public","relation":"research_paper"}]},"author":[{"first_name":"Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"}],"file":[{"file_size":14376,"content_type":"application/zip","creator":"system","access_level":"open_access","file_name":"IST-2018-111-v1+1_CODES.zip","checksum":"97992e3e8cf8544ec985a48971708726","date_updated":"2020-07-14T12:47:08Z","date_created":"2018-12-12T13:05:13Z","relation":"main_file","file_id":"5641"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:41Z","date_updated":"2024-02-21T13:45:39Z","_id":"5587","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"status":"public","ddc":["530"],"title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","ec_funded":1,"abstract":[{"text":"Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to PLoS ONE 10.4 e0122670 (2015).","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:08Z","type":"research_data","datarep_id":"111"}]