[{"keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"has_accepted_license":"1","article_processing_charge":"No","day":"10","month":"12","oa":1,"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"},"citation":{"mla":"Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930.","short":"B. Kavcic, (2020).","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930.","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8930.","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8930","ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020."},"date_published":"2020-12-10T00:00:00Z","doi":"10.15479/AT:ISTA:8930","type":"research_data","license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"file_date_updated":"2020-12-09T15:00:19Z","department":[{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","ddc":["570"],"status":"public","_id":"8930","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","oa_version":"Published Version","file":[{"file_id":"8932","relation":"main_file","success":1,"checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","date_updated":"2020-12-09T15:00:19Z","date_created":"2020-12-09T15:00:19Z","access_level":"open_access","file_name":"PLoSCompBiol2020_datarep.zip","creator":"bkavcic","file_size":315494370,"content_type":"application/zip"}],"date_created":"2020-12-09T15:04:02Z","date_updated":"2024-02-21T12:41:42Z","contributor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","contributor_type":"supervisor","last_name":"Tkačik"},{"first_name":"Tobias","last_name":"Bollenbach","contributor_type":"supervisor","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"8997","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X","first_name":"Bor","last_name":"Kavcic"}]},{"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"},"citation":{"ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951","ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951.","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951","mla":"Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951.","short":"A.A. Nagy-Staron, (2020).","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951."},"oa":1,"doi":"10.15479/AT:ISTA:8951","date_published":"2020-12-21T00:00:00Z","keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"article_processing_charge":"No","has_accepted_license":"1","day":"21","month":"12","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","ddc":["570"],"status":"public","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8951","year":"2020","file":[{"date_updated":"2020-12-20T09:52:52Z","date_created":"2020-12-20T09:52:52Z","success":1,"checksum":"f57862aeee1690c7effd2b1117d40ed1","file_id":"8952","relation":"main_file","creator":"bkavcic","file_size":523,"content_type":"text/plain","file_name":"readme.txt","access_level":"open_access"},{"file_size":379228,"content_type":"application/octet-stream","creator":"bkavcic","file_name":"GRNs Research depository.gb","access_level":"open_access","date_created":"2020-12-20T22:01:44Z","date_updated":"2020-12-20T22:01:44Z","checksum":"f2c6d5232ec6d551b6993991e8689e9f","success":1,"relation":"main_file","file_id":"8954"}],"oa_version":"Published Version","date_updated":"2024-02-21T12:41:57Z","date_created":"2020-12-20T10:00:26Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"9283"}]},"contributor":[{"first_name":"Anna A","last_name":"Nagy-Staron","contributor_type":"project_member","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","last_name":"Tomasek","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","last_name":"Caruso Carter","first_name":"Caroline"},{"last_name":"Sonnleitner","contributor_type":"project_member","first_name":"Elisabeth"},{"first_name":"Bor","last_name":"Kavcic","contributor_type":"project_member","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6041-254X"},{"contributor_type":"project_member","last_name":"Paixão","first_name":"Tiago"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","contributor_type":"project_manager"}],"author":[{"full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron","first_name":"Anna A","orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","file_date_updated":"2020-12-20T22:01:44Z","abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks."}]},{"month":"01","day":"28","article_processing_charge":"No","has_accepted_license":"1","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"doi":"10.15479/AT:ISTA:7383","date_published":"2020-01-28T00:00:00Z","citation":{"short":"R. Grah, (2020).","mla":"Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383.","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.","ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7383","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7383."},"oa":1,"abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:57Z","type":"research_data","author":[{"full_name":"Grah, Rok","first_name":"Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560"}],"contributor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","contributor_type":"project_leader","last_name":"Guet"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7652"}]},"date_updated":"2024-02-21T12:42:31Z","date_created":"2020-01-28T10:41:49Z","file":[{"file_id":"7384","relation":"main_file","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-28T10:39:40Z","checksum":"9d292cf5207b3829225f44c044cdb3fd","file_name":"Scripts.zip","access_level":"open_access","creator":"rgrah","content_type":"application/zip","file_size":73363365},{"creator":"rgrah","content_type":"text/plain","file_size":962,"file_name":"READ_ME_MAIN.txt","access_level":"open_access","date_updated":"2020-07-14T12:47:57Z","date_created":"2020-01-28T10:39:30Z","checksum":"4076ceab32ef588cc233802bab24c1ab","file_id":"7385","relation":"main_file"}],"oa_version":"Published Version","year":"2020","_id":"7383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"type":"research_data","license":"https://creativecommons.org/publicdomain/zero/1.0/","file_date_updated":"2021-03-10T07:31:50Z","title":"Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling","status":"public","ddc":["530"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GeKa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9222","year":"2020","date_created":"2021-03-05T18:00:47Z","date_updated":"2024-02-21T12:42:13Z","file":[{"access_level":"open_access","file_name":"DOI_SiteControlledHWs.zip","creator":"gkatsaro","file_size":13317557,"content_type":"application/x-zip-compressed","file_id":"9223","relation":"main_file","checksum":"41b66e195ed3dbd73077feee77b05652","date_created":"2021-03-05T17:50:45Z","date_updated":"2021-03-05T17:50:45Z"},{"date_updated":"2021-03-10T07:31:50Z","date_created":"2021-03-10T07:31:50Z","success":1,"checksum":"a1dc5f710ba4b3bb7f248195ba754ab2","file_id":"9233","relation":"main_file","creator":"dernst","content_type":"text/plain","file_size":3515,"file_name":"Readme.txt","access_level":"open_access"}],"oa_version":"Published Version","author":[{"full_name":"Katsaros, Georgios","last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"contributor":[{"last_name":"Katsaros","contributor_type":"research_group","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"7541","status":"public","relation":"used_in_publication"}]},"day":"16","month":"03","article_processing_charge":"No","has_accepted_license":"1","citation":{"chicago":"Katsaros, Georgios. “Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:9222.","mla":"Katsaros, Georgios. Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:9222.","short":"G. Katsaros, (2020).","ista":"Katsaros G. 2020. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9222.","ieee":"G. Katsaros, “Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling.” Institute of Science and Technology Austria, 2020.","apa":"Katsaros, G. (2020). Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9222","ama":"Katsaros G. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. 2020. doi:10.15479/AT:ISTA:9222"},"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:9222","date_published":"2020-03-16T00:00:00Z"},{"month":"09","day":"21","has_accepted_license":"1","article_processing_charge":"No","project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"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"},"citation":{"ieee":"R. Guseinov, “Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter.’” Institute of Science and Technology Austria, 2020.","apa":"Guseinov, R. (2020). Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8375","ista":"Guseinov R. 2020. Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8375.","ama":"Guseinov R. Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” 2020. doi:10.15479/AT:ISTA:8375","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8375.","short":"R. Guseinov, (2020).","mla":"Guseinov, Ruslan. Supplementary Data for “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8375."},"oa":1,"doi":"10.15479/AT:ISTA:8375","date_published":"2020-09-21T00:00:00Z","type":"research_data","abstract":[{"lang":"eng","text":"Supplementary movies showing the following sequences for spatio-temporarily programmed shells: input geometry and actuation time landscape; comparison of morphing processes from a camera recording and a simulation; final actuated shape."}],"file_date_updated":"2020-09-11T09:52:36Z","ec_funded":1,"ddc":["000"],"status":"public","title":"Supplementary data for \"Computational design of curved thin shells: from glass façades to programmable matter\"","department":[{"_id":"BeBi"}],"publisher":"Institute of Science and Technology Austria","year":"2020","_id":"8375","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-11T09:52:54Z","date_updated":"2024-02-21T12:44:29Z","oa_version":"Published Version","file":[{"date_created":"2020-09-11T09:45:21Z","date_updated":"2020-09-11T09:45:21Z","success":1,"checksum":"4029ffd65fb82ef2366b2fc2a4908e16","file_id":"8376","relation":"main_file","creator":"rguseino","content_type":"video/mp4","file_size":29214988,"file_name":"supplementary_movie_1.mp4","access_level":"open_access"},{"access_level":"open_access","file_name":"supplementary_movie_2.mp4","creator":"rguseino","content_type":"video/mp4","file_size":28449475,"file_id":"8377","relation":"main_file","success":1,"checksum":"8ed03b04d80f1a4e622cb22e6100afd8","date_updated":"2020-09-11T09:45:25Z","date_created":"2020-09-11T09:45:25Z"},{"content_type":"video/mp4","file_size":26315853,"creator":"rguseino","file_name":"supplementary_movie_3.mp4","access_level":"open_access","date_updated":"2020-09-11T09:45:28Z","date_created":"2020-09-11T09:45:28Z","checksum":"ad6864afb5e694e5c52a88fba4e02eea","success":1,"relation":"main_file","file_id":"8378"},{"access_level":"open_access","file_name":"supplementary_movie_4.mp4","content_type":"video/mp4","file_size":25198755,"creator":"rguseino","relation":"main_file","file_id":"8379","checksum":"b079cef7871fe1afb69af0e2b099f3b1","success":1,"date_created":"2020-09-11T09:45:33Z","date_updated":"2020-09-11T09:45:33Z"},{"date_updated":"2020-09-11T09:45:36Z","date_created":"2020-09-11T09:45:36Z","success":1,"checksum":"9d1d48a8ed5c109a999c51b044ee523d","file_id":"8380","relation":"main_file","creator":"rguseino","file_size":29011354,"content_type":"video/mp4","file_name":"supplementary_movie_5.mp4","access_level":"open_access"},{"date_created":"2020-09-11T09:52:36Z","date_updated":"2020-09-11T09:52:36Z","success":1,"checksum":"d414d0059e982d752d218756b3c3ce05","file_id":"8381","relation":"main_file","creator":"rguseino","file_size":586,"content_type":"text/plain","file_name":"readme.txt","access_level":"open_access"}],"author":[{"first_name":"Ruslan","last_name":"Guseinov","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","full_name":"Guseinov, Ruslan"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8366"}]},"contributor":[{"id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9819-5077","first_name":"Ruslan","contributor_type":"researcher","last_name":"Guseinov"},{"first_name":"Connor","contributor_type":"researcher","last_name":"McMahan"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Perez Rodriguez","first_name":"Jesus"},{"first_name":"Chiara","last_name":"Daraio","contributor_type":"researcher"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","contributor_type":"researcher","first_name":"Bernd"}]},{"project":[{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"},{"_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235","call_identifier":"FWF","name":"Towards scalable hut wire quantum devices"}],"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,"citation":{"chicago":"Katsaros, Georgios. “Supplementary Data for ‘Zero Field Splitting of Heavy-Hole States in Quantum Dots.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7689.","mla":"Katsaros, Georgios. Supplementary Data for “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7689.","short":"G. Katsaros, (2020).","ista":"Katsaros G. 2020. Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7689.","ieee":"G. Katsaros, “Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots.’” Institute of Science and Technology Austria, 2020.","apa":"Katsaros, G. (2020). Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7689","ama":"Katsaros G. 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All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. 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Supplementary Data for “Computational Design of Cold Bent Glass Façades.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8761."},"oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"date_published":"2020-11-23T00:00:00Z","doi":"10.15479/AT:ISTA:8761","month":"11","day":"23","has_accepted_license":"1","article_processing_charge":"No"},{"type":"research_data","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-10-19T10:12:29Z","abstract":[{"text":"Supplementary data provided for the provided for the publication:\r\nIgor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. 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Csicsvari, I. Gridchyn, P. Schönenberger, (2020).","mla":"Csicsvari, Jozsef L., et al. Optogenetic Alteration of Hippocampal Network Activity. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8563.","apa":"Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8563","ieee":"J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020.","ista":"Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563.","ama":"Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:10.15479/AT:ISTA:8563"},"doi":"10.15479/AT:ISTA:8563","date_published":"2020-10-19T00:00:00Z"},{"date_published":"2020-12-01T00:00:00Z","doi":"10.15479/AT:ISTA:14592","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"citation":{"chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592.","mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592.","short":"F.K. Schur, (2020).","ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592.","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592"},"oa":1,"has_accepted_license":"1","article_processing_charge":"No","day":"01","month":"12","oa_version":"Published Version","file":[{"creator":"fschur","file_size":49297,"content_type":"application/zip","access_level":"open_access","file_name":"3Dprint-files_download_v2.zip","success":1,"checksum":"0108616e2a59e51879ea51299a29b091","date_created":"2023-11-22T14:58:44Z","date_updated":"2023-11-22T14:58:44Z","file_id":"14593","relation":"main_file"},{"content_type":"text/plain","file_size":641,"creator":"cchlebak","file_name":"readme.txt","access_level":"open_access","date_created":"2023-12-01T10:39:59Z","date_updated":"2023-12-01T10:39:59Z","checksum":"4c66ddedee4d01c1c4a7978208350cfc","success":1,"relation":"main_file","file_id":"14637"}],"date_updated":"2024-02-21T12:44:48Z","date_created":"2023-11-22T15:00:57Z","contributor":[{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Fäßler","first_name":"Florian"},{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","first_name":"Bettina","last_name":"Zens","contributor_type":"researcher"},{"last_name":"Hauschild","contributor_type":"researcher","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","first_name":"Florian KM","last_name":"Schur","contributor_type":"researcher"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"8586"}]},"author":[{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"department":[{"_id":"FlSc"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["570"],"title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14592","year":"2020","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2023-12-01T10:39:59Z","abstract":[{"lang":"eng","text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications."}],"type":"research_data"},{"author":[{"full_name":"Tomanek, Isabella","last_name":"Tomanek","first_name":"Isabella","orcid":"0000-0001-6197-363X","id":"3981F020-F248-11E8-B48F-1D18A9856A87"}],"contributor":[{"first_name":"Calin C","last_name":"Guet","contributor_type":"project_leader","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"related_material":{"record":[{"id":"7652","relation":"used_in_publication","status":"public"}]},"date_updated":"2024-02-21T12:45:25Z","date_created":"2019-11-13T09:07:31Z","oa_version":"Published Version","file":[{"file_name":"D8_S35_R2_001.fastq","description":"Illumina whole genome sequence data for Locus 1 - amplified.","access_level":"open_access","creator":"itomanek","file_size":2456192500,"content_type":"application/octet-stream","file_id":"7017","title":"Locus1_amplified","relation":"main_file","date_updated":"2020-07-14T12:47:47Z","date_created":"2019-11-13T08:52:21Z","checksum":"72441055043eda4cbf1398a422e2c118"},{"content_type":"application/octet-stream","file_size":2833452234,"creator":"itomanek","file_name":"IT028_S11_R2_001.fastq","description":"Illumina whole genome sequence data for Locus 1 - 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However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"type":"research_data","doi":"10.15479/AT:ISTA:7016","date_published":"2019-11-13T00:00:00Z","citation":{"chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016.","short":"I. Tomanek, (2019).","ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.","ieee":"I. 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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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","lang":"eng"}],"datarep_id":"98","type":"research_data","doi":"10.15479/AT:ISTA:98","date_published":"2018-03-29T00:00:00Z","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":{"ista":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, 10.15479/AT:ISTA:98.","ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","apa":"Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., & Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:98","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:10.15479/AT:ISTA:98","chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:98.","mla":"Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:98.","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018)."},"oa":1,"project":[{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF"}],"month":"03","day":"29","has_accepted_license":"1","article_processing_charge":"No","keyword":["retina","decoding","regression","neural networks","complex stimulus"]},{"citation":{"short":"B. Vicoso, (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.","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. 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Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 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.","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."},"doi":"10.15479/AT:ISTA:95","date_published":"2018-02-12T00:00:00Z","day":"12","month":"02","article_processing_charge":"No","has_accepted_license":"1","title":"Data and Python scripts supporting Python package FAPS","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"_id":"5583","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","date_created":"2018-12-12T12:31:39Z","date_updated":"2024-02-21T13:45:01Z","file":[{"file_id":"5606","relation":"main_file","date_created":"2018-12-12T13:02:41Z","date_updated":"2020-07-14T12:47:07Z","checksum":"fc6aab51439f2622ba6df8632e66fd4f","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","access_level":"open_access","creator":"system","content_type":"text/csv","file_size":122048},{"file_id":"5607","relation":"main_file","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:42Z","checksum":"92347586ae4f8a6eb7c04354797bf314","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","access_level":"open_access","creator":"system","content_type":"text/csv","file_size":235980},{"file_size":311712,"content_type":"text/csv","creator":"system","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","access_level":"open_access","date_created":"2018-12-12T13:02:43Z","date_updated":"2020-07-14T12:47:07Z","checksum":"3300813645a54e6c5c39f41917228354","relation":"main_file","file_id":"5608"},{"access_level":"open_access","file_name":"IST-2018-95-v1+4_faps_scripts.zip","creator":"system","content_type":"application/zip","file_size":342090,"file_id":"5609","relation":"main_file","checksum":"e739fc473567fd8f39438b445fc46147","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:44Z"}],"oa_version":"Published Version","author":[{"first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"286"}]},"datarep_id":"95","type":"research_data","file_date_updated":"2020-07-14T12:47:07Z","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"}]},{"keyword":["microscopy","microfluidics"],"day":"07","month":"02","has_accepted_license":"1","article_processing_charge":"No","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":{"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.","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.","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)."},"oa":1,"date_published":"2018-02-07T00:00:00Z","doi":"10.15479/AT:ISTA:74","datarep_id":"74","type":"research_data","file_date_updated":"2020-07-14T12:47:04Z","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"}],"publist_id":"7385","_id":"5569","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","ddc":["579"],"status":"public","title":"Time-lapse microscopy data","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","author":[{"first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"last_name":"Nikolic","first_name":"Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela"}],"related_material":{"record":[{"id":"438","relation":"research_paper","status":"public"}]},"date_updated":"2024-02-21T13:44:45Z","date_created":"2018-12-12T12:31:35Z","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:04:39Z","checksum":"61ebb92213cfffeba3ddbaff984b81af","file_id":"5637","relation":"main_file","creator":"system","content_type":"application/zip","file_size":3558703796,"file_name":"IST-2018-74-v1+2_15-11-05.zip","access_level":"open_access"},{"file_size":1830422606,"content_type":"application/zip","creator":"system","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","relation":"main_file","file_id":"5638"},{"checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","date_updated":"2020-07-14T12:47:04Z","date_created":"2018-12-12T13:05:11Z","file_id":"5639","relation":"main_file","creator":"system","content_type":"application/zip","file_size":2140849248,"access_level":"open_access","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip"}]},{"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":{"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.","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.","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.","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.","ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:10.15479/AT:ISTA:62"},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"date_published":"2018-09-21T00:00:00Z","doi":"10.15479/AT:ISTA:62","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"article_processing_charge":"No","has_accepted_license":"1","month":"09","day":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5587","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"ddc":["530"],"title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","status":"public","related_material":{"record":[{"id":"161","status":"public","relation":"research_paper"}]},"author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","first_name":"Daniele","last_name":"De Martino","full_name":"De Martino, Daniele"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"file":[{"date_updated":"2020-07-14T12:47:08Z","date_created":"2018-12-12T13:05:13Z","checksum":"97992e3e8cf8544ec985a48971708726","relation":"main_file","file_id":"5641","content_type":"application/zip","file_size":14376,"creator":"system","file_name":"IST-2018-111-v1+1_CODES.zip","access_level":"open_access"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:45:39Z","date_created":"2018-12-12T12:31:41Z","type":"research_data","datarep_id":"111","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"},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila 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Version","date_created":"2018-12-19T14:22:35Z","date_updated":"2024-02-21T13:59:18Z","contributor":[{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","first_name":"Gemma","last_name":"Puixeu Sala"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"6089","status":"public","relation":"research_paper"}]},"author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"}],"type":"research_data","ec_funded":1,"file_date_updated":"2020-07-14T12:47:11Z","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."}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"citation":{"chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757.","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).","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.","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","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"},"oa":1,"doi":"10.15479/at:ista:/5757","date_published":"2018-12-19T00:00:00Z","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"article_processing_charge":"No","has_accepted_license":"1","month":"12","day":"19"},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:07Z","abstract":[{"lang":"eng","text":"Mean repression values and standard error of the mean are given for all operator mutant libraries."}],"type":"research_data","datarep_id":"108","oa_version":"Published Version","file":[{"file_name":"IST-2018-108-v1+1_data_figures.xlsx","access_level":"open_access","creator":"system","file_size":16507,"content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_id":"5611","relation":"main_file","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:45Z","checksum":"1435781526c77413802adee0d4583cce"}],"date_created":"2018-12-12T12:31:40Z","date_updated":"2024-03-28T23:30:49Z","related_material":{"record":[{"id":"67","relation":"research_paper","status":"public"},{"status":"public","relation":"research_paper","id":"6371"}]},"author":[{"id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia","last_name":"Igler","full_name":"Igler, Claudia"},{"full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","ddc":["576"],"status":"public","title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","_id":"5585","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","has_accepted_license":"1","month":"07","day":"20","date_published":"2018-07-20T00:00:00Z","doi":"10.15479/AT:ISTA:108","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"},{"grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"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":{"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.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","mla":"Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:108.","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","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","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.","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"}},{"date_created":"2018-12-12T12:31:33Z","date_updated":"2024-02-21T13:46:14Z","oa_version":"Published Version","file":[{"creator":"system","file_size":1336936,"content_type":"application/octet-stream","access_level":"open_access","file_name":"IST-2017-61-v1+1_bint_fishmovie32_100.mat","checksum":"e620eff260646f57b479a69492c8b765","date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:03:04Z","file_id":"5622","relation":"main_file"},{"date_updated":"2020-07-14T12:47:03Z","date_created":"2018-12-12T13:03:05Z","checksum":"de83f9b81ea0aae3cddfc3ed982e0759","file_id":"5623","relation":"main_file","creator":"system","content_type":"application/zip","file_size":1897543,"file_name":"IST-2017-61-v1+2_bint_fishmovie32_100.zip","access_level":"open_access"}],"author":[{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"},{"first_name":"Dario","last_name":"Amodei","full_name":"Amodei, Dario"},{"full_name":"Schneidman, Elad","last_name":"Schneidman","first_name":"Elad"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"last_name":"Berry","first_name":"Michael","full_name":"Berry, Michael"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"2257"}]},"title":"Multi-electrode array recording from salamander retinal ganglion cells","ddc":["570"],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"}],"year":"2017","_id":"5562","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:03Z","abstract":[{"text":"This data was collected as part of the study [1]. 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.","lang":"eng"}],"datarep_id":"61","type":"research_data","doi":"10.15479/AT:ISTA:61","date_published":"2017-02-27T00:00:00Z","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":{"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","ieee":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode array recording from salamander retinal ganglion cells.” Institute of Science and Technology Austria, 2017.","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","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.","short":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017).","mla":"Marre, Olivier, et al. Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells. Institute of Science and Technology Austria, 2017, doi: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."},"oa":1,"day":"27","month":"02","has_accepted_license":"1","article_processing_charge":"No","keyword":["multi-electrode recording","retinal ganglion cells"]},{"month":"02","day":"13","has_accepted_license":"1","article_processing_charge":"No","keyword":["graph matching","feature matching","QAP","MAP-inference"],"date_published":"2017-02-13T00:00:00Z","doi":"10.15479/AT:ISTA:57","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,"citation":{"chicago":"Kainmueller, Dagmar, Florian Jug, Carsten Rother, and Gene Meyers. “Graph Matching Problems for Annotating C. Elegans.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:57.","mla":"Kainmueller, Dagmar, et al. Graph Matching Problems for Annotating C. Elegans. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:57.","short":"D. Kainmueller, F. Jug, C. Rother, G. Meyers, (2017).","ista":"Kainmueller D, Jug F, Rother C, Meyers G. 2017. Graph matching problems for annotating C. Elegans, Institute of Science and Technology Austria, 10.15479/AT:ISTA:57.","apa":"Kainmueller, D., Jug, F., Rother, C., & Meyers, G. (2017). Graph matching problems for annotating C. Elegans. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:57","ieee":"D. Kainmueller, F. Jug, C. Rother, and G. Meyers, “Graph matching problems for annotating C. Elegans.” Institute of Science and Technology Austria, 2017.","ama":"Kainmueller D, Jug F, Rother C, Meyers G. Graph matching problems for annotating C. Elegans. 2017. doi:10.15479/AT:ISTA:57"},"abstract":[{"text":"Graph matching problems as described in \"Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans.\" by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. 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"}],"file_date_updated":"2020-07-14T12:47:03Z","datarep_id":"57","type":"research_data","author":[{"full_name":"Kainmueller, Dagmar","first_name":"Dagmar","last_name":"Kainmueller"},{"full_name":"Jug, Florian","last_name":"Jug","first_name":"Florian"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"},{"last_name":"Meyers","first_name":"Gene","full_name":"Meyers, Gene"}],"date_created":"2018-12-12T12:31:32Z","date_updated":"2024-02-21T13:46:31Z","oa_version":"Published Version","file":[{"checksum":"3dc3e1306a66028a34181ebef2923139","date_created":"2018-12-12T13:02:54Z","date_updated":"2020-07-14T12:47:03Z","file_id":"5614","relation":"main_file","creator":"system","file_size":327042819,"content_type":"application/zip","access_level":"open_access","file_name":"IST-2017-57-v1+1_wormMatchingProblems.zip"}],"_id":"5561","acknowledgement":"We thank Vladimir Kolmogorov and Stephan Saalfeld forinspiring discussions.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","ddc":["000"],"status":"public","title":"Graph matching problems for annotating C. Elegans","department":[{"_id":"VlKo"}],"publisher":"Institute of Science and Technology Austria"},{"month":"03","day":"20","article_processing_charge":"No","has_accepted_license":"1","citation":{"chicago":"Lukacisin, Martin. “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, 2017. https://doi.org/10.15479/AT:ISTA:64.","short":"M. Lukacisin, (2017).","mla":"Lukacisin, Martin. 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, 2017, doi:10.15479/AT:ISTA:64.","apa":"Lukacisin, M. (2017). 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:64","ieee":"M. Lukacisin, “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, 2017.","ista":"Lukacisin M. 2017. 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:64.","ama":"Lukacisin M. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2017. doi:10.15479/AT:ISTA:64"},"tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa":1,"date_published":"2017-03-20T00:00:00Z","doi":"10.15479/AT:ISTA:64","datarep_id":"64","type":"research_data","file_date_updated":"2020-07-14T12:47:03Z","abstract":[{"lang":"eng","text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. 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The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. \r\nThe Video is licensed under a CC BY NC ND license. 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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)"}],"file_date_updated":"2020-07-14T12:47:00Z","publist_id":"5828","_id":"5550","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Flower colour data and phylogeny (NEXUS) files","ddc":["576"],"status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"author":[{"first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"1382"}]},"date_updated":"2024-02-21T13:49:54Z","date_created":"2018-12-12T12:31:29Z","file":[{"file_id":"5594","relation":"main_file","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T13:02:27Z","checksum":"950f85b80427d357bfeff09608ba02e9","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","access_level":"open_access","creator":"system","file_size":4468543,"content_type":"application/zip"}],"oa_version":"Published Version","month":"02","day":"19","article_processing_charge":"No","has_accepted_license":"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)"},"oa":1,"citation":{"chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:34.","short":"T. 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Fiji script to determine average speed and direction of migration of cells, Institute of Science and Technology Austria, 10.15479/AT:ISTA:44."},"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,"file_date_updated":"2020-07-14T12:47:02Z","abstract":[{"text":"This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.","lang":"eng"}],"datarep_id":"44","type":"research_data","date_created":"2018-12-12T12:31:31Z","date_updated":"2024-02-21T13:50:06Z","oa_version":"Published Version","file":[{"creator":"system","file_size":20692,"content_type":"application/zip","file_name":"IST-2016-44-v1+1_migrationAnalyzer.zip","access_level":"open_access","date_updated":"2020-07-14T12:47:02Z","date_created":"2018-12-12T13:03:03Z","checksum":"9f96cddbcd4ed689f48712ffe234d5e5","file_id":"5621","relation":"main_file"}],"author":[{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"}],"status":"public","title":"Fiji script to determine average speed and direction of migration of cells","ddc":["570"],"department":[{"_id":"Bio"}],"publisher":"Institute of Science and Technology Austria","year":"2016","_id":"5555","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"doi":"10.15479/AT:ISTA:46","date_published":"2016-09-20T00:00:00Z","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":{"chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:46.","short":"P. Swoboda, (2016).","mla":"Swoboda, Paul. Synthetic Discrete Tomography Problems. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:46.","apa":"Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:46","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016.","ista":"Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science and Technology Austria, 10.15479/AT:ISTA:46.","ama":"Swoboda P. Synthetic discrete tomography problems. 2016. doi:10.15479/AT:ISTA:46"},"oa":1,"has_accepted_license":"1","article_processing_charge":"No","month":"09","day":"20","keyword":["discrete tomography"],"contributor":[{"first_name":"Jan","contributor_type":"data_collector","last_name":"Kuske"}],"author":[{"full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda"}],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip","creator":"system","content_type":"application/zip","file_size":36058401,"file_id":"5645","relation":"main_file","checksum":"aa5a16a0dc888da7186fb8fc45e88439","date_created":"2018-12-12T13:05:19Z","date_updated":"2020-07-14T12:47:02Z"}],"date_updated":"2024-02-21T13:50:21Z","date_created":"2018-12-12T12:31:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5557","year":"2016","department":[{"_id":"VlKo"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["006"],"title":"Synthetic discrete tomography problems","abstract":[{"text":"Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and 256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:02Z","type":"research_data","datarep_id":"46"},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","status":"public","ddc":["576"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5553","year":"2016","oa_version":"Published Version","file":[{"file_id":"5620","relation":"main_file","checksum":"4ae751b1fa4897fa216241f975a57313","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:02Z","access_level":"open_access","file_name":"IST-2016-37-v1+1_paternity_archive.zip","creator":"system","content_type":"application/zip","file_size":132808}],"date_updated":"2024-02-21T13:51:14Z","date_created":"2018-12-12T12:31:30Z","contributor":[{"first_name":"Nicholas H","last_name":"Barton","contributor_type":"project_manager","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"related_material":{"record":[{"id":"1398","status":"public","relation":"research_paper"}]},"author":[{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"full_name":"Ellis, Thomas","last_name":"Ellis","first_name":"Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","datarep_id":"37","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"}],"file_date_updated":"2020-07-14T12:47:01Z","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,"citation":{"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","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.","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","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.","short":"D. Field, T. Ellis, (2016).","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."},"date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:37","keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"has_accepted_license":"1","article_processing_charge":"No","day":"19","month":"02"},{"author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis","full_name":"Ellis, Thomas"}],"related_material":{"record":[{"id":"1398","status":"public","relation":"research_paper"}]},"contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"date_created":"2018-12-12T12:31:29Z","date_updated":"2024-02-21T13:51:27Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5640","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","date_created":"2018-12-12T13:05:12Z","date_updated":"2020-07-14T12:47:01Z","access_level":"open_access","file_name":"IST-2016-35-v1+1_array_data.zip","content_type":"application/zip","file_size":32775,"creator":"system"}],"year":"2016","_id":"5551","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Data on pollinator observations and offpsring phenotypes","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:01Z","abstract":[{"lang":"eng","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."}],"datarep_id":"35","type":"research_data","date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:35","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,"citation":{"ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi: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.","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","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","mla":"Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.","short":"T. Ellis, (2016).","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."},"month":"02","day":"19","has_accepted_license":"1","article_processing_charge":"No"},{"date_published":"2016-02-19T00:00:00Z","doi":"10.15479/AT:ISTA:36","citation":{"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","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","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.","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:10.15479/AT:ISTA:36","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.","short":"T. Ellis, (2016).","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."},"oa":1,"article_processing_charge":"No","has_accepted_license":"1","day":"19","month":"02","related_material":{"record":[{"id":"1398","status":"public","relation":"research_paper"}]},"contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"author":[{"full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","last_name":"Ellis"}],"file":[{"relation":"main_file","file_id":"5625","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:07Z","checksum":"cbc61b523d4d475a04a737d50dc470ef","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","access_level":"open_access","content_type":"application/zip","file_size":44905,"creator":"system"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:30Z","date_updated":"2024-02-21T13:51:40Z","_id":"5552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","status":"public","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."}],"file_date_updated":"2020-07-14T12:47:01Z","type":"research_data","datarep_id":"36"},{"article_processing_charge":"No","has_accepted_license":"1","day":"12","month":"05","keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"doi":"10.15479/AT:ISTA:43","date_published":"2016-05-12T00:00:00Z","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,"citation":{"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.","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","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:10.15479/AT:ISTA:43","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.","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.","short":"M. Tugrul, (2016)."},"file_date_updated":"2020-07-14T12:47:01Z","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"}],"type":"research_data","datarep_id":"43","file":[{"file_id":"5626","relation":"main_file","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:08Z","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","access_level":"open_access","creator":"system","file_size":1123495,"content_type":"application/zip"}],"oa_version":"Published Version","date_created":"2018-12-12T12:31:30Z","date_updated":"2024-02-21T13:50:34Z","contributor":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","last_name":"Steinrück","first_name":"Magdalena"},{"id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","first_name":"Fabienne","contributor_type":"researcher","last_name":"Jesse"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1131"}]},"author":[{"full_name":"Tugrul, Murat","last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5554","year":"2016"},{"author":[{"full_name":"Bojsen-Hansen, Morten","first_name":"Morten","last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4417-3224"}],"pubrep_id":"640","related_material":{"record":[{"id":"1122","status":"public","relation":"other"}]},"date_created":"2018-12-12T12:31:31Z","date_updated":"2024-02-21T13:50:48Z","file":[{"relation":"main_file","file_id":"5589","checksum":"5b1b256ad796fbddb4b7729f5e45e444","date_created":"2018-12-12T13:02:18Z","date_updated":"2020-07-14T12:47:02Z","access_level":"open_access","file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2","file_size":55237885,"content_type":"application/x-bzip2","creator":"system"}],"oa_version":"Published Version","_id":"5558","year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["004"],"title":"Tracking, Correcting and Absorbing Water Surface Waves","department":[{"_id":"ChWo"}],"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"PhD thesis LaTeX source code","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:02Z","publist_id":"6238","datarep_id":"48","type":"research_data","doi":"10.15479/AT:ISTA:48","date_published":"2016-09-23T00:00:00Z","citation":{"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.","mla":"Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:48.","short":"M. Bojsen-Hansen, (2016).","ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 10.15479/AT:ISTA:48.","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016.","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","ama":"Bojsen-Hansen M. 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(2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions","lang":"eng"}],"department":[{"_id":"ToBo"}],"publisher":"Institute of Science and Technology Austria","status":"public","ddc":["571"],"title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","year":"2016","_id":"5556","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"IST-2016-45-v1+1_PaperCode.zip","content_type":"application/zip","file_size":296722548,"creator":"system","relation":"main_file","file_id":"5616","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","date_created":"2018-12-12T13:02:58Z","date_updated":"2020-07-14T12:47:02Z"}],"oa_version":"Published Version","date_updated":"2024-02-21T13:51:53Z","date_created":"2018-12-12T12:31:31Z","related_material":{"record":[{"id":"8431","relation":"used_in_publication","status":"deleted"},{"relation":"research_paper","status":"public","id":"1029"}]},"author":[{"orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisin","first_name":"Martin","full_name":"Lukacisin, Martin"},{"full_name":"Landon, Matthieu","first_name":"Matthieu","last_name":"Landon"},{"full_name":"Jajoo, Rishi","last_name":"Jajoo","first_name":"Rishi"}],"keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"article_processing_charge":"No","has_accepted_license":"1","month":"08","day":"25","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"citation":{"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","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.","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","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.","short":"M. Lukacisin, M. Landon, R. Jajoo, (2016).","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.","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."},"oa":1,"date_published":"2016-08-25T00:00:00Z","doi":"10.15479/AT:ISTA:45"},{"file_date_updated":"2020-07-14T12:47:00Z","publist_id":"5564","ec_funded":1,"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","year":"2015","date_created":"2018-12-12T12:31:29Z","date_updated":"2024-02-21T13:52:07Z","author":[{"first_name":"Andreas","last_name":"Fellner","id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","full_name":"Fellner, Andreas"}],"contributor":[{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"1603","relation":"popular_science","status":"public"}]},"month":"08","project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"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)"},"doi":"10.15479/AT:ISTA:28","datarep_id":"28","type":"research_data","abstract":[{"lang":"eng","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."}],"ddc":["004"],"status":"public","title":"Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5549","file":[{"relation":"main_file","file_id":"5597","checksum":"b8bcb43c0893023cda66c1b69c16ac62","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T13:02:31Z","access_level":"open_access","file_name":"IST-2015-28-v1+2_Fellner_DataRep.zip","file_size":49557109,"content_type":"application/zip","creator":"system"}],"oa_version":"Published Version","keyword":["Markov Decision Process","Decision Tree","Probabilistic Verification","Counterexample Explanation"],"day":"13","article_processing_charge":"No","has_accepted_license":"1","citation":{"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.","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","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.","short":"A. Fellner, (2015).","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.","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."},"date_published":"2015-08-13T00:00:00Z"}]