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Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}],"has_accepted_license":"1","doi":"10.15479/AT:ISTA:95","file_date_updated":"2020-07-14T12:47:07Z","type":"research_data","file":[{"content_type":"text/csv","date_updated":"2020-07-14T12:47:07Z","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","access_level":"open_access","creator":"system","file_size":122048,"date_created":"2018-12-12T13:02:41Z","relation":"main_file","checksum":"fc6aab51439f2622ba6df8632e66fd4f","file_id":"5606"},{"content_type":"text/csv","date_updated":"2020-07-14T12:47:07Z","access_level":"open_access","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","creator":"system","file_size":235980,"date_created":"2018-12-12T13:02:42Z","relation":"main_file","checksum":"92347586ae4f8a6eb7c04354797bf314","file_id":"5607"},{"date_updated":"2020-07-14T12:47:07Z","content_type":"text/csv","file_id":"5608","checksum":"3300813645a54e6c5c39f41917228354","relation":"main_file","file_size":311712,"date_created":"2018-12-12T13:02:43Z","creator":"system","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","access_level":"open_access"},{"checksum":"e739fc473567fd8f39438b445fc46147","file_id":"5609","creator":"system","access_level":"open_access","file_name":"IST-2018-95-v1+4_faps_scripts.zip","relation":"main_file","file_size":342090,"date_created":"2018-12-12T13:02:44Z","date_updated":"2020-07-14T12:47:07Z","content_type":"application/zip"}],"article_processing_charge":"No","citation":{"apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","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.","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.","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95"},"title":"Data and Python scripts supporting Python package FAPS","date_created":"2018-12-12T12:31:39Z","_id":"5583","related_material":{"record":[{"relation":"research_paper","id":"286","status":"public"}]},"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_version":"Published Version","contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"datarep_id":"95","license":"https://creativecommons.org/publicdomain/zero/1.0/","status":"public","department":[{"_id":"NiBa"}],"day":"12","year":"2018","date_updated":"2024-02-21T13:45:01Z","date_published":"2018-02-12T00:00:00Z","month":"02"},{"year":"2018","publist_id":"7385","date_updated":"2024-02-21T13:44:45Z","department":[{"_id":"CaGu"}],"status":"public","keyword":["microscopy","microfluidics"],"day":"07","month":"02","date_published":"2018-02-07T00:00:00Z","has_accepted_license":"1","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:04Z","doi":"10.15479/AT:ISTA:74","type":"research_data","file":[{"content_type":"application/zip","date_updated":"2020-07-14T12:47:04Z","creator":"system","file_name":"IST-2018-74-v1+2_15-11-05.zip","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T13:04:39Z","file_size":3558703796,"checksum":"61ebb92213cfffeba3ddbaff984b81af","file_id":"5637"},{"date_created":"2018-12-12T13:04:55Z","file_size":1830422606,"relation":"main_file","access_level":"open_access","file_name":"IST-2018-74-v1+3_15-07-31.zip","creator":"system","file_id":"5638","checksum":"bf26649af310ef6892d68576515cde6d","content_type":"application/zip","date_updated":"2020-07-14T12:47:04Z"},{"creator":"system","access_level":"open_access","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","relation":"main_file","file_size":2140849248,"date_created":"2018-12-12T13:05:11Z","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","file_id":"5639","content_type":"application/zip","date_updated":"2020-07-14T12:47:04Z"}],"publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","first_name":"Tobias"},{"last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","first_name":"Nela","orcid":"0000-0001-9068-6090"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"438"}]},"_id":"5569","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_version":"Published Version","datarep_id":"74","ddc":["579"],"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).","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:10.15479/AT:ISTA:74","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 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","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."},"article_processing_charge":"No","date_created":"2018-12-12T12:31:35Z","title":"Time-lapse microscopy data"},{"external_id":{"isi":["000440149300021"]},"date_published":"2018-07-30T00:00:00Z","language":[{"iso":"eng"}],"month":"07","isi":1,"day":"30","license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2024-02-21T13:45:39Z","quality_controlled":"1","article_processing_charge":"No","article_number":"2988","ddc":["570"],"_id":"161","author":[{"full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","orcid":"0000-0002-5214-4706","first_name":"Daniele"},{"full_name":"Mc, Andersson Anna","last_name":"Mc","first_name":"Andersson Anna"},{"orcid":"0000-0001-5396-4346","first_name":"Tobias","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C"},{"orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"publisher":"Springer Nature","type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":9,"issue":"1","publication":"Nature Communications","intvolume":" 9","publication_status":"published","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"status":"public","publist_id":"7760","year":"2018","title":"Statistical mechanics for metabolic networks during steady state growth","date_created":"2018-12-11T11:44:57Z","citation":{"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.","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.","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"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5587"}]},"ec_funded":1,"oa":1,"project":[{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:06Z","date_created":"2018-12-17T16:44:28Z","file_size":1043205,"relation":"main_file","access_level":"open_access","file_name":"2018_NatureComm_DeMartino.pdf","creator":"dernst","file_id":"5728","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18"}],"file_date_updated":"2020-07-14T12:45:06Z","doi":"10.1038/s41467-018-05417-9","abstract":[{"lang":"eng","text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"author":[{"first_name":"Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele"},{"orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik"}],"oa":1,"publisher":"Institute of Science and Technology Austria","file":[{"relation":"main_file","file_size":14376,"date_created":"2018-12-12T13:05:13Z","creator":"system","access_level":"open_access","file_name":"IST-2018-111-v1+1_CODES.zip","file_id":"5641","checksum":"97992e3e8cf8544ec985a48971708726","content_type":"application/zip","date_updated":"2020-07-14T12:47:08Z"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"type":"research_data","doi":"10.15479/AT:ISTA:62","file_date_updated":"2020-07-14T12:47:08Z","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)."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","date_created":"2018-12-12T12:31:41Z","article_processing_charge":"No","citation":{"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).","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.","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","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."},"oa_version":"Published Version","datarep_id":"111","ddc":["530"],"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)"},"_id":"5587","related_material":{"record":[{"relation":"research_paper","id":"161","status":"public"}]},"ec_funded":1,"day":"21","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"department":[{"_id":"GaTk"}],"status":"public","date_updated":"2024-02-21T13:45:39Z","year":"2018","date_published":"2018-09-21T00:00:00Z","month":"09"},{"scopus_import":"1","type":"journal_article","volume":208,"has_accepted_license":"1","author":[{"last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kelemen, Réka K","first_name":"Réka K","orcid":"0000-0002-8489-9281"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"publisher":"Genetics Society of America","ddc":["576"],"_id":"542","quality_controlled":"1","article_processing_charge":"No","date_updated":"2024-02-21T13:48:27Z","day":"01","month":"01","isi":1,"external_id":{"isi":["000419356300024"]},"date_published":"2018-01-01T00:00:00Z","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425"}],"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:46:50Z","creator":"system","access_level":"open_access","file_name":"IST-2018-1058-v1+1_365.full__1_.pdf","relation":"main_file","date_created":"2018-12-12T10:15:14Z","file_size":1311661,"checksum":"2123845e7031a0cf043905be160f9e69","file_id":"5132"}],"doi":"10.1534/genetics.117.300513","file_date_updated":"2020-07-14T12:46:50Z","abstract":[{"text":"The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"365 - 375","article_type":"original","oa":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"id":"5571","status":"public","relation":"popular_science"},{"relation":"popular_science","id":"5572","status":"public"}]},"ec_funded":1,"title":"Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver","date_created":"2018-12-11T11:47:04Z","citation":{"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.","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.","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.","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"},"publist_id":"7274","year":"2018","publication_status":"published","department":[{"_id":"BeVi"}],"status":"public","pubrep_id":"1058","publication":"Genetics","intvolume":" 208","issue":"1"}]