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Heuristic prediction for multiple stresses. 2017. doi:10.1371/journal.pcbi.1005609.s003","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","mla":"Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003."},"article_processing_charge":"No","date_created":"2021-08-09T14:08:14Z","title":"Heuristic prediction for multiple stresses","_id":"9851","related_material":{"record":[{"status":"public","id":"696","relation":"used_in_publication"}]},"oa_version":"Published Version","author":[{"last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","first_name":"Marta","orcid":"0000-0002-2519-8004"},{"last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian","first_name":"Sebastian"},{"orcid":"0000-0003-2361-3953","first_name":"Tiago","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao"}],"publisher":"Public Library of Science","doi":"10.1371/journal.pcbi.1005609.s003","abstract":[{"text":"Based on the intuitive derivation of the dynamics of SIM allele frequency pM in the main text, we present a heuristic prediction for the long-term SIM allele frequencies with χ > 1 stresses and compare it to numerical simulations.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference"},{"status":"public","department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"day":"18","year":"2017","date_updated":"2023-02-23T12:55:39Z","date_published":"2017-07-18T00:00:00Z","month":"07","publisher":"Public Library of Science","author":[{"first_name":"Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta"},{"first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","first_name":"Tiago"}],"abstract":[{"text":"We show how different combination strategies affect the fraction of individuals that are multi-resistant.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.1371/journal.pcbi.1005609.s004","type":"research_data_reference","citation":{"chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies for Different Combination Strategies.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s004.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. 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Paixao, (2017)."},"article_processing_charge":"No","date_created":"2021-08-09T14:11:40Z","title":"Resistance frequencies for different combination strategies","related_material":{"record":[{"status":"public","id":"696","relation":"used_in_publication"}]},"_id":"9852","oa_version":"Published Version"},{"date_published":"2017-12-18T00:00:00Z","month":"12","department":[{"_id":"CaGu"}],"status":"public","day":"18","year":"2017","date_updated":"2023-02-23T12:25:04Z","article_processing_charge":"No","citation":{"chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures and Tables.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s018.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. 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Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s018."},"title":"Source data for figures and tables","date_created":"2021-08-09T13:27:16Z","_id":"9844","related_material":{"record":[{"relation":"used_in_publication","id":"541","status":"public"}]},"oa_version":"Published Version","publisher":"Public Library of Science","author":[{"last_name":"Nikolic","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","orcid":"0000-0001-9068-6090"},{"first_name":"Frank","full_name":"Schreiber, Frank","last_name":"Schreiber"},{"last_name":"Dal Co","full_name":"Dal Co, Alma","first_name":"Alma"},{"first_name":"Daniel","full_name":"Kiviet, Daniel","last_name":"Kiviet"},{"first_name":"Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"full_name":"Littmann, Sten","last_name":"Littmann","first_name":"Sten"},{"full_name":"Kuypers, Marcel","last_name":"Kuypers","first_name":"Marcel"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.1371/journal.pgen.1007122.s018","type":"research_data_reference"},{"main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2017.0646","open_access":"1"}],"related_material":{"record":[{"id":"9847","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"202"}]},"oa_version":"Published Version","citation":{"mla":"Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:10.1098/rsbl.2017.0646.","short":"M. Pleska, C.C. Guet, Biology Letters 13 (2017).","ama":"Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0646","apa":"Pleska, M., & Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2017.0646","ieee":"M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” Biology Letters, vol. 13, no. 12. The Royal Society, 2017.","ista":"Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646.","chicago":"Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters. The Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0646."},"date_created":"2018-12-11T11:47:11Z","title":"Effects of mutations in phage restriction sites during escape from restriction–modification","doi":"10.1098/rsbl.2017.0646","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage l and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape.","lang":"eng"}],"project":[{"grant_number":"RGY0079/2011","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","_id":"251BCBEC-B435-11E9-9278-68D0E5697425"},{"grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"oa":1,"article_type":"original","intvolume":" 13","publication":"Biology Letters","issue":"12","publist_id":"7253","year":"2017","status":"public","department":[{"_id":"CaGu"}],"publication_status":"published","_id":"561","publication_identifier":{"issn":["1744-9561"]},"article_number":"20170646","pmid":1,"acknowledgement":"This work was funded by an HFSP Young Investigators' grant RGY0079/2011 (C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria.","article_processing_charge":"No","quality_controlled":"1","volume":13,"type":"journal_article","scopus_import":"1","author":[{"last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","first_name":"Maros","orcid":"0000-0001-7460-7479"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"publisher":"The Royal Society","month":"12","language":[{"iso":"eng"}],"external_id":{"pmid":["29237814"]},"date_published":"2017-12-01T00:00:00Z","date_updated":"2023-09-07T11:59:32Z","day":"01"},{"article_processing_charge":"No","acknowledgement":"During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n","supervisor":[{"orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet"}],"publication_identifier":{"issn":["2663-337X"]},"_id":"202","ddc":["576","579"],"publisher":"Institute of Science and Technology Austria","author":[{"id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","last_name":"Pleska","orcid":"0000-0001-7460-7479","first_name":"Maros"}],"has_accepted_license":"1","type":"dissertation","language":[{"iso":"eng"}],"date_published":"2017-10-01T00:00:00Z","month":"10","day":"01","date_updated":"2023-09-15T12:04:56Z","alternative_title":["ISTA Thesis"],"citation":{"mla":"Pleska, Maros. Biology of Restriction-Modification Systems at the Single-Cell and Population Level. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_916.","short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017.","ama":"Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:10.15479/AT:ISTA:th_916","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","apa":"Pleska, M. (2017). Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_916","chicago":"Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916.","ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria."},"title":"Biology of restriction-modification systems at the single-cell and population level","date_created":"2018-12-11T11:45:10Z","related_material":{"record":[{"status":"public","id":"1243","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"561","status":"public"},{"status":"public","id":"457","relation":"part_of_dissertation"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","oa":1,"page":"126","abstract":[{"lang":"eng","text":"Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:45:24Z","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_916","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:24Z","relation":"main_file","file_size":18569590,"date_created":"2018-12-12T10:08:48Z","creator":"system","access_level":"open_access","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","file_id":"4710","checksum":"33cfb59674e91f82e3738396d3fb3776"},{"date_updated":"2020-07-14T12:45:24Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"dcc239968decb233e7f98cf1083d8c26","file_id":"6204","creator":"dernst","access_level":"closed","file_name":"2017_Pleska_Maros_Thesis.docx","relation":"source_file","date_created":"2019-04-05T08:33:14Z","file_size":2801649}],"project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","grant_number":"24210"}],"pubrep_id":"916","department":[{"_id":"CaGu"}],"status":"public","publication_status":"published","year":"2017","publist_id":"7711"},{"day":"01","date_updated":"2023-09-20T11:06:03Z","external_id":{"isi":["000414343200003"]},"date_published":"2017-12-01T00:00:00Z","language":[{"iso":"eng"}],"month":"12","isi":1,"author":[{"last_name":"Giacobbe","full_name":"Giacobbe, Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco","orcid":"0000-0001-8180-0904"},{"orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet"},{"first_name":"Ashutosh","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"first_name":"Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"orcid":"0000-0002-9041-0905","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana","last_name":"Petrov"}],"publisher":"Springer","type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":54,"quality_controlled":"1","article_processing_charge":"No","ddc":["006","576"],"_id":"1351","publication_identifier":{"issn":["00015903"]},"publication_status":"published","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"status":"public","publist_id":"5898","year":"2017","issue":"8","pubrep_id":"649","publication":"Acta Informatica","intvolume":" 54","page":"765 - 787","oa":1,"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"},{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"file":[{"date_updated":"2020-07-14T12:44:46Z","content_type":"application/pdf","checksum":"4e661d9135d7f8c342e8e258dee76f3e","file_id":"5841","file_name":"2017_ActaInformatica_Giacobbe.pdf","access_level":"open_access","creator":"dernst","file_size":755241,"date_created":"2019-01-17T15:57:29Z","relation":"main_file"}],"doi":"10.1007/s00236-016-0278-x","file_date_updated":"2020-07-14T12:44:46Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights.","lang":"eng"}],"title":"Model checking the evolution of gene regulatory networks","date_created":"2018-12-11T11:51:32Z","citation":{"ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” Acta Informatica, vol. 54, no. 8. Springer, pp. 765–787, 2017.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica. Springer. https://doi.org/10.1007/s00236-016-0278-x","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787. doi:10.1007/s00236-016-0278-x"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"id":"1835","status":"public","relation":"earlier_version"}]},"ec_funded":1},{"language":[{"iso":"eng"}],"date_published":"2017-06-01T00:00:00Z","external_id":{"isi":["000400379500013"]},"isi":1,"month":"06","day":"01","date_updated":"2023-09-20T11:14:42Z","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["01784617"]},"_id":"1336","ddc":["576"],"publisher":"Springer","author":[{"last_name":"Paixao","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","orcid":"0000-0003-2361-3953"},{"last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge","first_name":"Jorge"},{"first_name":"Dirk","full_name":"Sudholt, Dirk","last_name":"Sudholt"},{"first_name":"Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","full_name":"Trubenova, Barbora"}],"has_accepted_license":"1","volume":78,"type":"journal_article","scopus_import":"1","issue":"2","intvolume":" 78","publication":"Algorithmica","pubrep_id":"658","status":"public","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","year":"2017","publist_id":"5931","citation":{"ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.","chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica. Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1.","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” Algorithmica, vol. 78, no. 2. Springer, pp. 681–713, 2017.","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. Algorithmica. Springer. https://doi.org/10.1007/s00453-016-0212-1","ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 2017;78(2):681-713. doi:10.1007/s00453-016-0212-1","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:10.1007/s00453-016-0212-1."},"title":"Towards a runtime comparison of natural and artificial evolution","date_created":"2018-12-11T11:51:27Z","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","oa":1,"page":"681 - 713","abstract":[{"lang":"eng","text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:44:44Z","doi":"10.1007/s00453-016-0212-1","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:44:44Z","creator":"system","access_level":"open_access","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","relation":"main_file","file_size":710206,"date_created":"2018-12-12T10:10:19Z","checksum":"7873f665a0c598ac747c908f34cb14b9","file_id":"4805"}],"project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}]},{"oa_version":"None","date_created":"2018-12-11T11:50:03Z","title":"Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis","citation":{"ieee":"C. Fang et al., “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” Molecular Microbiology, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017.","apa":"Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., & Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.13597","chicago":"Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology. Wiley-Blackwell, 2017. https://doi.org/10.1111/mmi.13597.","ista":"Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31.","short":"C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31.","mla":"Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:10.1111/mmi.13597.","ama":"Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 2017;104(1):16-31. doi:10.1111/mmi.13597"},"abstract":[{"lang":"eng","text":"BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1111/mmi.13597","page":"16 - 31","publication":"Molecular Microbiology","intvolume":" 104","issue":"1","year":"2017","publist_id":"6294","publication_status":"published","department":[{"_id":"CaGu"}],"status":"public","publication_identifier":{"issn":[" 0950382X"]},"_id":"1084","quality_controlled":"1","article_processing_charge":"No","type":"journal_article","scopus_import":"1","volume":104,"publisher":"Wiley-Blackwell","author":[{"full_name":"Fang, Chong","last_name":"Fang","first_name":"Chong"},{"orcid":"0000-0002-1391-8377","first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron"},{"first_name":"Martin","last_name":"Grafe","full_name":"Grafe, Martin"},{"full_name":"Heermann, Ralf","last_name":"Heermann","first_name":"Ralf"},{"first_name":"Kirsten","last_name":"Jung","full_name":"Jung, Kirsten"},{"last_name":"Gebhard","full_name":"Gebhard, Susanne","first_name":"Susanne"},{"first_name":"Thorsten","last_name":"Mascher","full_name":"Mascher, Thorsten"}],"month":"04","isi":1,"date_published":"2017-04-01T00:00:00Z","external_id":{"isi":["000398059200002"]},"language":[{"iso":"eng"}],"date_updated":"2023-09-20T11:48:43Z","day":"01"},{"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1,"date_created":"2018-12-11T11:49:23Z","title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element","citation":{"ieee":"M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192","ista":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.","chicago":"Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.","mla":"Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192.","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).","ama":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192"},"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:48:16Z","creator":"system","file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf","access_level":"open_access","relation":"main_file","file_size":2441529,"date_created":"2018-12-12T10:17:49Z","checksum":"59cdd4400fb41280122d414fea971546","file_id":"5306"},{"date_updated":"2020-07-14T12:48:16Z","content_type":"application/pdf","checksum":"b69024880558b858eb8c5d47a92b6377","file_id":"5307","access_level":"open_access","file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf","creator":"system","file_size":3752660,"date_created":"2018-12-12T10:17:50Z","relation":"main_file"}],"project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091"},{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:48:16Z","doi":"10.7554/eLife.25192","abstract":[{"lang":"eng","text":"Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"pubrep_id":"841","publication":"eLife","intvolume":" 6","publist_id":"6460","year":"2017","publication_status":"published","status":"public","department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"article_number":"e25192","ddc":["576"],"_id":"954","publication_identifier":{"issn":["2050084X"]},"quality_controlled":"1","article_processing_charge":"Yes","type":"journal_article","scopus_import":"1","has_accepted_license":"1","volume":6,"author":[{"first_name":"Mato","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","orcid":"0000-0003-2361-3953","first_name":"Tiago"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton"},{"full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612","first_name":"Jonathan P"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"publisher":"eLife Sciences Publications","month":"05","isi":1,"external_id":{"isi":["000404024800001"]},"date_published":"2017-05-18T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2023-09-22T10:01:17Z","day":"18"},{"date_updated":"2023-10-17T08:51:18Z","day":"01","isi":1,"month":"06","language":[{"iso":"eng"}],"date_published":"2017-06-01T00:00:00Z","external_id":{"isi":["000403513900006"]},"has_accepted_license":"1","volume":"81C","scopus_import":"1","type":"journal_article","publisher":"International Federation of Automatic Control","author":[{"first_name":"Moritz","last_name":"Lang","full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sontag","full_name":"Sontag, Eduardo","first_name":"Eduardo"}],"publication_identifier":{"issn":["0005-1098"]},"_id":"1007","ddc":["000"],"article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","year":"2017","publist_id":"6391","status":"public","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publication_status":"published","publication":"Automatica","pubrep_id":"813","abstract":[{"text":"A nonlinear system possesses an invariance with respect to a set of transformations if its output dynamics remain invariant when transforming the input, and adjusting the initial condition accordingly. Most research has focused on invariances with respect to time-independent pointwise transformations like translational-invariance (u(t) -> u(t) + p, p in R) or scale-invariance (u(t) -> pu(t), p in R>0). In this article, we introduce the concept of s0-invariances with respect to continuous input transformations exponentially growing/decaying over time. We show that s0-invariant systems not only encompass linear time-invariant (LTI) systems with transfer functions having an irreducible zero at s0 in R, but also that the input/output relationship of nonlinear s0-invariant systems possesses properties well known from their linear counterparts. Furthermore, we extend the concept of s0-invariances to second- and higher-order s0-invariances, corresponding to invariances with respect to transformations of the time-derivatives of the input, and encompassing LTI systems with zeros of multiplicity two or higher. Finally, we show that nth-order 0-invariant systems realize – under mild conditions – nth-order nonlinear differential operators: when excited by an input of a characteristic functional form, the system’s output converges to a constant value only depending on the nth (nonlinear) derivative of the input.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2018-12-12T10:11:29Z","doi":"10.1016/j.automatica.2017.03.030","file":[{"content_type":"application/pdf","date_updated":"2018-12-12T10:11:29Z","relation":"main_file","date_created":"2018-12-12T10:11:29Z","file_size":1401954,"creator":"system","access_level":"open_access","file_name":"IST-2017-813-v1+1_ZerosOfNonlinearSystems.pdf","file_id":"4884"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"oa":1,"page":"46 - 55","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","citation":{"chicago":"Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.” Automatica. International Federation of Automatic Control, 2017. https://doi.org/10.1016/j.automatica.2017.03.030.","ista":"Lang M, Sontag E. 2017. Zeros of nonlinear systems with input invariances. Automatica. 81C, 46–55.","apa":"Lang, M., & Sontag, E. (2017). Zeros of nonlinear systems with input invariances. Automatica. International Federation of Automatic Control. https://doi.org/10.1016/j.automatica.2017.03.030","ieee":"M. Lang and E. Sontag, “Zeros of nonlinear systems with input invariances,” Automatica, vol. 81C. International Federation of Automatic Control, pp. 46–55, 2017.","ama":"Lang M, Sontag E. Zeros of nonlinear systems with input invariances. Automatica. 2017;81C:46-55. doi:10.1016/j.automatica.2017.03.030","short":"M. Lang, E. Sontag, Automatica 81C (2017) 46–55.","mla":"Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.” Automatica, vol. 81C, International Federation of Automatic Control, 2017, pp. 46–55, doi:10.1016/j.automatica.2017.03.030."},"title":"Zeros of nonlinear systems with input invariances","date_created":"2018-12-11T11:49:39Z"},{"publisher":"Institute of Science and Technology Austria","oa":1,"author":[{"first_name":"Magdalena","orcid":"0000-0003-1229-9719","last_name":"Steinrück","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","full_name":"Steinrück, Magdalena"},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Compressed Fastq files with whole-genome sequencing data of IS-wt strain D and clones from four evolved populations (A11, C08, C10, D08). Information on this data collection is available in the Methods Section of the primary publication."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:03Z","doi":"10.15479/AT:ISTA:65","type":"research_data","file":[{"date_updated":"2020-07-14T12:47:03Z","content_type":"application/zip","file_id":"5627","checksum":"31a0c01d022721073241a23d192cc37e","relation":"main_file","file_size":1225959109,"date_created":"2018-12-12T13:03:18Z","creator":"system","access_level":"open_access","file_name":"IST-2017-65-v1+1_D_anc_1.fastq.zip"},{"file_id":"5628","checksum":"d8f26f83ce7e7e45436121f9c6cd9b83","file_size":1422656107,"date_created":"2018-12-12T13:03:30Z","relation":"main_file","access_level":"open_access","file_name":"IST-2017-65-v1+1_D_anc_2.fastq.zip","creator":"system","date_updated":"2020-07-14T12:47:03Z","content_type":"application/zip"},{"date_updated":"2020-07-14T12:47:03Z","content_type":"application/zip","file_id":"5629","checksum":"e07b99bcfe55b5f132ca03b8b48c8cbc","relation":"main_file","date_created":"2018-12-12T13:03:33Z","file_size":565014975,"creator":"system","file_name":"IST-2017-65-v1+2_D_A11_1.fastq.zip","access_level":"open_access"},{"checksum":"eda86143d5f32d844b54f8530041e32b","file_id":"5630","access_level":"open_access","file_name":"IST-2017-65-v1+3_D_A11_2.fastq.zip","creator":"system","file_size":564490030,"date_created":"2018-12-12T13:03:42Z","relation":"main_file","date_updated":"2020-07-14T12:47:03Z","content_type":"application/zip"},{"date_updated":"2020-07-14T12:47:03Z","content_type":"application/zip","checksum":"906d44f950c1626d9b99f34fbf89cb12","file_id":"5631","creator":"system","access_level":"open_access","file_name":"IST-2017-65-v1+4_D_C10_1.fastq.zip","relation":"main_file","date_created":"2018-12-12T13:03:46Z","file_size":875430169},{"file_id":"5632","checksum":"6ca14a032a79e0c787106bdf635725c9","relation":"main_file","file_size":638298201,"date_created":"2018-12-12T13:03:54Z","creator":"system","file_name":"IST-2017-65-v1+6_D_C08_2.fastq.zip","access_level":"open_access","date_updated":"2020-07-14T12:47:03Z","content_type":"application/zip"},{"date_created":"2018-12-12T13:04:01Z","file_size":894702866,"relation":"main_file","access_level":"open_access","file_name":"IST-2017-65-v1+5_D_C10_2.fastq.zip","creator":"system","file_id":"5633","checksum":"66ab16ddb5ba64b2e263ef746ebf2893","content_type":"application/zip","date_updated":"2020-07-14T12:47:03Z"},{"creator":"system","access_level":"open_access","file_name":"IST-2017-65-v1+7_D_C08_1.fastq.zip","relation":"main_file","date_created":"2018-12-12T13:04:07Z","file_size":623648989,"checksum":"82607970174f8d37773b7d3acc712195","file_id":"5634","content_type":"application/zip","date_updated":"2020-07-14T12:47:03Z"},{"content_type":"application/zip","date_updated":"2020-07-14T12:47:03Z","file_size":259359583,"date_created":"2018-12-12T13:04:11Z","relation":"main_file","file_name":"IST-2017-65-v1+8_D_D08_1.fastq.zip","access_level":"open_access","creator":"system","file_id":"5635","checksum":"225c30b243268c7dda9d6f8327933252"}],"citation":{"chicago":"Steinrück, Magdalena, and Calin C Guet. “Fastq Files for ‘Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.’” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:65.","ista":"Steinrück M, Guet CC. 2017. Fastq files for ‘Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:65.","ieee":"M. Steinrück and C. C. Guet, “Fastq files for ‘Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.’” Institute of Science and Technology Austria, 2017.","apa":"Steinrück, M., & Guet, C. C. (2017). Fastq files for “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:65","ama":"Steinrück M, Guet CC. Fastq files for “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection.” 2017. doi:10.15479/AT:ISTA:65","mla":"Steinrück, Magdalena, and Calin C. Guet. Fastq Files for “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:65.","short":"M. Steinrück, C.C. Guet, (2017)."},"article_processing_charge":"No","date_created":"2018-12-12T12:31:33Z","title":"Fastq files for \"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection\"","related_material":{"record":[{"relation":"research_paper","id":"704","status":"public"}]},"_id":"5564","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa_version":"Published Version","datarep_id":"65","ddc":["576"],"department":[{"_id":"CaGu"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","status":"public","day":"11","year":"2017","date_updated":"2024-02-21T13:47:28Z","date_published":"2017-04-11T00:00:00Z","month":"04"},{"oa":1,"author":[{"first_name":"Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"orcid":"0000-0003-2912-6769","first_name":"Anna M","full_name":"Andersson, Anna M","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","last_name":"Andersson"},{"orcid":"0000-0003-3768-877X","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin","last_name":"Tomasek"},{"first_name":"Enrique","last_name":"Balleza","full_name":"Balleza, Enrique"},{"first_name":"Daniel","full_name":"Kiviet, Daniel","last_name":"Kiviet"},{"first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052"}],"publisher":"Institute of Science and Technology Austria","file":[{"content_type":"application/zip","date_updated":"2020-07-14T12:47:03Z","creator":"system","access_level":"open_access","file_name":"IST-2017-53-v1+1_Data_MDE.zip","relation":"main_file","date_created":"2018-12-12T13:02:38Z","file_size":6773204,"checksum":"d77859af757ac8025c50c7b12b52eaf3","file_id":"5603"}],"type":"research_data","file_date_updated":"2020-07-14T12:47:03Z","doi":"10.15479/AT:ISTA:53","abstract":[{"lang":"eng","text":"This repository contains the data collected for the manuscript \"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity\".\r\nThe data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication.\r\nData is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic \"mother machine\" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication."}],"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T12:31:32Z","title":"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity","citation":{"chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:53.","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:53.","ieee":"T. Bergmiller et al., “Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity.” Institute of Science and Technology Austria, 2017.","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:53","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:10.15479/AT:ISTA:53","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, (2017).","mla":"Bergmiller, Tobias, et al. Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:53."},"article_processing_charge":"No","oa_version":"Published Version","datarep_id":"53","ddc":["571"],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"_id":"5560","related_material":{"record":[{"relation":"research_paper","status":"public","id":"665"}]},"day":"10","keyword":["single cell microscopy","mother machine microfluidic device","AcrAB-TolC pump","multi-drug efflux","Escherichia coli"],"status":"public","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"date_updated":"2024-02-21T13:49:00Z","year":"2017","date_published":"2017-03-10T00:00:00Z","month":"03"},{"article_type":"original","page":"311 - 315","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria."}],"doi":"10.1126/science.aaf4762","project":[{"call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 2017;356(6335):311-315. doi:10.1126/science.aaf4762","mla":"Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:10.1126/science.aaf4762.","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.","chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aaf4762.","ieee":"T. Bergmiller et al., “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” Science, vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315, 2017.","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaf4762"},"date_created":"2018-12-11T11:47:48Z","title":"Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity","related_material":{"record":[{"id":"5560","status":"public","relation":"popular_science"}]},"oa_version":"None","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"status":"public","publication_status":"published","year":"2017","publist_id":"7064","issue":"6335","intvolume":" 356","publication":"Science","publisher":"American Association for the Advancement of Science","author":[{"orcid":"0000-0001-5396-4346","first_name":"Tobias","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller"},{"first_name":"Anna M","orcid":"0000-0003-2912-6769","last_name":"Andersson","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","full_name":"Andersson, Anna M"},{"last_name":"Tomasek","full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","orcid":"0000-0003-3768-877X"},{"full_name":"Balleza, Enrique","last_name":"Balleza","first_name":"Enrique"},{"first_name":"Daniel","last_name":"Kiviet","full_name":"Kiviet, Daniel"},{"last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052"}],"volume":356,"scopus_import":1,"type":"journal_article","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["00368075"]},"_id":"665","day":"21","date_updated":"2024-02-21T13:49:00Z","language":[{"iso":"eng"}],"date_published":"2017-04-21T00:00:00Z","month":"04"},{"publication_status":"published","status":"public","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"year":"2017","publist_id":"6362","issue":"16","publication":"Angewandte Chemie - International Edition","intvolume":" 56","page":"4608-4611","oa":1,"project":[{"call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets [do not use to be deleted]","grant_number":"W1232-B24","call_identifier":"FWF"}],"file":[{"success":1,"date_updated":"2019-01-18T09:39:55Z","content_type":"application/pdf","file_id":"5845","relation":"main_file","date_created":"2019-01-18T09:39:55Z","file_size":2614942,"creator":"dernst","access_level":"open_access","file_name":"2017_communications_Kainrath.pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes."}],"doi":"10.1002/anie.201611998","file_date_updated":"2019-01-18T09:39:55Z","title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","date_created":"2018-12-11T11:49:46Z","citation":{"ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998","mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition, vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:10.1002/anie.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie - International Edition 56 (2017) 4608–4611.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition. Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998.","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie - International Edition, vol. 56, no. 16. Wiley-Blackwell, pp. 4608–4611, 2017.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201611998"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"status":"public","id":"418","relation":"dissertation_contains"},{"relation":"part_of_dissertation","id":"7680","status":"public"}]},"day":"20","date_updated":"2024-03-18T23:30:13Z","date_published":"2017-03-20T00:00:00Z","external_id":{"isi":["000398154000038"]},"language":[{"iso":"eng"}],"month":"03","isi":1,"publisher":"Wiley-Blackwell","author":[{"last_name":"Kainrath","full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie"},{"full_name":"Stadler, Manuela","last_name":"Stadler","first_name":"Manuela"},{"last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","full_name":"Gschaider-Reichhart, Eva","first_name":"Eva","orcid":"0000-0002-7218-7738"},{"first_name":"Martin","last_name":"Distel","full_name":"Distel, Martin"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","first_name":"Harald L"}],"scopus_import":"1","type":"journal_article","has_accepted_license":"1","volume":56,"quality_controlled":"1","acknowledgement":"This work was supported by a grant from the European Unions Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)","article_processing_charge":"No","ddc":["540"],"publication_identifier":{"issn":["14337851"]},"_id":"1028"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","related_material":{"record":[{"id":"5564","status":"public","relation":"popular_science"},{"id":"26","status":"public","relation":"dissertation_contains"}]},"title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","date_created":"2018-12-11T11:48:01Z","citation":{"mla":"Steinrück, Magdalena, and Calin C. Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife, vol. 6, e25100, eLife Sciences Publications, 2017, doi:10.7554/eLife.25100.","short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","ama":"Steinrück M, Guet CC. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 2017;6. doi:10.7554/eLife.25100","ieee":"M. Steinrück and C. C. Guet, “Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Steinrück, M., & Guet, C. C. (2017). Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25100","chicago":"Steinrück, Magdalena, and Calin C Guet. “Complex Chromosomal Neighborhood Effects Determine the Adaptive Potential of a Gene under Selection.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25100.","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100."},"file":[{"file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","access_level":"open_access","creator":"system","file_size":2092088,"date_created":"2018-12-12T10:12:54Z","relation":"main_file","checksum":"6b908b5db9f61f6820ebd7f8fa815571","file_id":"4975","content_type":"application/pdf","date_updated":"2020-07-14T12:47:48Z"},{"file_id":"4976","checksum":"ca21530389b720243552678125fdba35","date_created":"2018-12-12T10:12:55Z","file_size":3428681,"relation":"main_file","access_level":"open_access","file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","creator":"system","date_updated":"2020-07-14T12:47:48Z","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data."}],"doi":"10.7554/eLife.25100","file_date_updated":"2020-07-14T12:47:48Z","oa":1,"publication":"eLife","pubrep_id":"890","intvolume":" 6","year":"2017","publist_id":"6990","publication_status":"published","status":"public","department":[{"_id":"CaGu"}],"ddc":["576"],"article_number":"e25100","publication_identifier":{"issn":["2050084X"]},"_id":"704","quality_controlled":"1","scopus_import":1,"type":"journal_article","volume":6,"has_accepted_license":"1","publisher":"eLife Sciences Publications","author":[{"first_name":"Magdalena","orcid":"0000-0003-1229-9719","last_name":"Steinrück","full_name":"Steinrück, Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","orcid":"0000-0001-6220-2052"}],"month":"07","date_published":"2017-07-25T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2024-03-18T23:30:28Z","day":"25"},{"title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","date_created":"2018-12-11T11:47:58Z","citation":{"ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 2017;13(7). doi:10.1371/journal.pcbi.1005609","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.","short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” PLoS Computational Biology, vol. 13, no. 7. Public Library of Science, 2017."},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"status":"public","id":"9849","relation":"research_data"},{"status":"public","id":"9850","relation":"research_data"},{"id":"9851","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9852"},{"relation":"dissertation_contains","id":"6263","status":"public"}]},"ec_funded":1,"article_type":"original","oa":1,"project":[{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:47:46Z","relation":"main_file","date_created":"2018-12-12T10:15:01Z","file_size":3775716,"creator":"system","access_level":"open_access","file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","file_id":"5117","checksum":"9143c290fa6458ed2563bff4b295554a"}],"doi":"10.1371/journal.pcbi.1005609","file_date_updated":"2020-07-14T12:47:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy.","lang":"eng"}],"issue":"7","pubrep_id":"894","publication":"PLoS Computational Biology","intvolume":" 13","publication_status":"published","status":"public","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"publist_id":"7004","year":"2017","quality_controlled":"1","article_number":"e1005609","ddc":["576"],"_id":"696","publication_identifier":{"issn":["1553734X"]},"author":[{"orcid":"0000-0002-2519-8004","first_name":"Marta","full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisinova"},{"first_name":"Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","first_name":"Tiago","orcid":"0000-0003-2361-3953"}],"publisher":"Public Library of Science","type":"journal_article","scopus_import":1,"has_accepted_license":"1","volume":13,"date_published":"2017-07-18T00:00:00Z","language":[{"iso":"eng"}],"month":"07","day":"18","date_updated":"2024-03-18T23:30:29Z"},{"issue":"2","intvolume":" 43","publication":"Developmental Cell","status":"public","department":[{"_id":"CaHe"},{"_id":"CaGu"},{"_id":"GaTk"}],"publication_status":"published","year":"2017","publist_id":"6934","citation":{"mla":"Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell, vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:10.1016/j.devcel.2017.09.014.","short":"V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora, C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.","ama":"Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 2017;43(2):198-211. doi:10.1016/j.devcel.2017.09.014","apa":"Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K., … Heisenberg, C.-P. J. (2017). An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.09.014","ieee":"V. Barone et al., “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” Developmental Cell, vol. 43, no. 2. Cell Press, pp. 198–211, 2017.","ista":"Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 43(2), 198–211.","chicago":"Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour, Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.09.014."},"title":"An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate","date_created":"2018-12-11T11:48:13Z","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"961","status":"public"},{"relation":"dissertation_contains","id":"8350","status":"public"}]},"oa_version":"None","page":"198 - 211","abstract":[{"text":"Cell-cell contact formation constitutes an essential step in evolution, leading to the differentiation of specialized cell types. However, remarkably little is known about whether and how the interplay between contact formation and fate specification affects development. Here, we identify a positive feedback loop between cell-cell contact duration, morphogen signaling, and mesendoderm cell-fate specification during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for ppl cell-fate specification. We further show that Nodal signaling promotes ppl cell-cell contact duration, generating a positive feedback loop between ppl cell-cell contact duration and cell-fate specification. Finally, by combining mathematical modeling and experimentation, we show that this feedback determines whether anterior axial mesendoderm cells become ppl or, instead, turn into endoderm. Thus, the interdependent activities of cell-cell signaling and contact formation control fate diversification within the developing embryo.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1016/j.devcel.2017.09.014","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"I2058","name":"Cell segregation in gastrulation: the role of cell fate specification","call_identifier":"FWF","_id":"252DD2A6-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"date_published":"2017-10-23T00:00:00Z","external_id":{"isi":["000413443700011"]},"isi":1,"month":"10","day":"23","date_updated":"2024-03-18T23:30:40Z","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["15345807"]},"_id":"735","publisher":"Cell Press","author":[{"id":"419EECCC-F248-11E8-B48F-1D18A9856A87","full_name":"Barone, Vanessa","last_name":"Barone","orcid":"0000-0003-2676-3367","first_name":"Vanessa"},{"first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz","last_name":"Lang"},{"first_name":"Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel"},{"full_name":"Pradhan, Saurabh","last_name":"Pradhan","first_name":"Saurabh"},{"first_name":"Shayan","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour"},{"full_name":"Sako, Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","last_name":"Sako","orcid":"0000-0002-6453-8075","first_name":"Keisuke"},{"first_name":"Mateusz K","last_name":"Sikora","full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"volume":43,"scopus_import":"1","type":"journal_article"},{"type":"journal_article","volume":5,"abstract":[{"text":"Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized the synthetic circuit using deterministic and stochastic mathematical models. Similar to its natural counterparts, our synthetic system shows bistable and hysteretic behavior, and the inducer concentration range for bistability as well as the switching rates between the two stable states depend on the repressor concentration. Our results indicate that a generic permease–inducer–repressor circuit with a single feedback loop is sufficient to explain the experimentally observed bistable behavior of the natural systems. We anticipate that the approach of reimplementing natural systems with orthogonal parts to identify crucial network components is applicable to other natural systems such as signaling pathways.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1021/acssynbio.6b00013","page":"1098 - 1107","publisher":"American Chemical Society","author":[{"first_name":"Robert","last_name":"Gnügge","full_name":"Gnügge, Robert"},{"first_name":"Lekshmi","full_name":"Dharmarajan, Lekshmi","last_name":"Dharmarajan"},{"first_name":"Moritz","last_name":"Lang","full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stelling, Jörg","last_name":"Stelling","first_name":"Jörg"}],"oa_version":"None","_id":"1008","quality_controlled":"1","date_created":"2018-12-11T11:49:40Z","title":"An orthogonal permease–inducer–repressor feedback loop shows bistability","acknowledgement":"We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı ́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor W. Schmidt for provision of and support with the micro fl uidic device, Markus Du ̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using “ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions, comments, and support.","citation":{"ista":"Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.","chicago":"Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” ACS Synthetic Biology. American Chemical Society, 2016. https://doi.org/10.1021/acssynbio.6b00013.","apa":"Gnügge, R., Dharmarajan, L., Lang, M., & Stelling, J. (2016). An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00013","ieee":"R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor feedback loop shows bistability,” ACS Synthetic Biology, vol. 5, no. 10. American Chemical Society, pp. 1098–1107, 2016.","ama":"Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 2016;5(10):1098-1107. doi:10.1021/acssynbio.6b00013","short":"R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.","mla":"Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” ACS Synthetic Biology, vol. 5, no. 10, American Chemical Society, 2016, pp. 1098–107, doi:10.1021/acssynbio.6b00013."},"year":"2016","publist_id":"6390","date_updated":"2021-01-12T06:47:37Z","day":"05","publication_status":"published","status":"public","department":[{"_id":"CaGu"}],"publication":"ACS Synthetic Biology","month":"05","intvolume":" 5","date_published":"2016-05-05T00:00:00Z","issue":"10","language":[{"iso":"eng"}]},{"publisher":"Society for Industrial and Applied Mathematics ","author":[{"full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang","first_name":"Moritz"},{"first_name":"Jörg","last_name":"Stelling","full_name":"Stelling, Jörg"}],"has_accepted_license":"1","volume":38,"scopus_import":1,"type":"journal_article","quality_controlled":"1","_id":"1170","ddc":["003","518","570","621"],"day":"15","date_updated":"2021-01-12T06:48:49Z","language":[{"iso":"eng"}],"date_published":"2016-11-15T00:00:00Z","month":"11","page":"B988 - B1008","abstract":[{"lang":"eng","text":"The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:44:37Z","doi":"10.1137/15M103306X","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:44:37Z","file_size":871964,"date_created":"2018-12-12T10:14:41Z","relation":"main_file","file_name":"IST-2017-811-v1+1_modular_parameter_identification.pdf","access_level":"local","creator":"system","file_id":"5095","checksum":"781bc3ffd30b2dd65b7727c5a285fc78"}],"citation":{"ama":"Lang M, Stelling J. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 2016;38(6):B988-B1008. doi:10.1137/15M103306X","short":"M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.","mla":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing, vol. 38, no. 6, Society for Industrial and Applied Mathematics , 2016, pp. B988–1008, doi:10.1137/15M103306X.","ista":"Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.","chicago":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics , 2016. https://doi.org/10.1137/15M103306X.","ieee":"M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society for Industrial and Applied Mathematics , pp. B988–B1008, 2016.","apa":"Lang, M., & Stelling, J. (2016). Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/15M103306X"},"title":"Modular parameter identification of biomolecular networks","date_created":"2018-12-11T11:50:31Z","oa_version":"Submitted Version","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"status":"public","publication_status":"published","year":"2016","publist_id":"6186","issue":"6","intvolume":" 38","publication":"SIAM Journal on Scientific Computing","pubrep_id":"811"},{"abstract":[{"lang":"eng","text":"Theoretical and numerical aspects of aerodynamic efficiency of propulsion systems coupled to the boundary layer of a fuselage are studied. We discuss the effects of local flow fields, which are affected both by conservative flow acceleration as well as total pressure losses, on the efficiency of boundary layer immersed propulsion devices. We introduce the concept of a boundary layer retardation turbine that helps reduce skin friction over the fuselage. We numerically investigate efficiency gains offered by boundary layer and wake interacting devices. We discuss the results in terms of a total energy consumption framework and show that efficiency gains of any device depend on all the other elements of the propulsion system."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.2514/6.2016-3764","type":"conference","scopus_import":1,"publisher":"AIAA","oa":1,"author":[{"last_name":"Mikić","full_name":"Mikić, Gregor","first_name":"Gregor"},{"last_name":"Stoll","full_name":"Stoll, Alex","first_name":"Alex"},{"first_name":"Joe","full_name":"Bevirt, Joe","last_name":"Bevirt"},{"first_name":"Rok","orcid":"0000-0003-2539-3560","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok"},{"first_name":"Mark","full_name":"Moore, Mark","last_name":"Moore"}],"page":"1 - 19","main_file_link":[{"url":"https://ntrs.nasa.gov/search.jsp?R=20160010167&hterms=Fuselage+boundary+layer+ingestion+propulsion+applied+thin+haul+commuter+aircraft+optimal+efficiency&qs=N%3D0%26Ntk%3DAll%26Ntt%3DFuselage%2520boundary%2520layer%2520ingestion%2520propulsion%2520applied%2520to%2520a%2520thin%2520haul%2520commuter%2520aircraft%2520for%2520optimal%2520efficiency%26Ntx%3Dmode%2520matchallpartial%26Nm%3D123%7CCollection%7CNASA%2520STI%7C%7C17%7CCollection%7CNACA","open_access":"1"}],"_id":"1220","oa_version":"Preprint","citation":{"ama":"Mikić G, Stoll A, Bevirt J, Grah R, Moore M. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. In: AIAA; 2016:1-19. doi:10.2514/6.2016-3764","mla":"Mikić, Gregor, et al. Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency. AIAA, 2016, pp. 1–19, doi:10.2514/6.2016-3764.","short":"G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.","chicago":"Mikić, Gregor, Alex Stoll, Joe Bevirt, Rok Grah, and Mark Moore. “Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency,” 1–19. AIAA, 2016. https://doi.org/10.2514/6.2016-3764.","ista":"Mikić G, Stoll A, Bevirt J, Grah R, Moore M. 2016. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. AIAA: Aviation Technology, Integration, and Operations Conference, 1–19.","apa":"Mikić, G., Stoll, A., Bevirt, J., Grah, R., & Moore, M. (2016). Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency (pp. 1–19). Presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA: AIAA. https://doi.org/10.2514/6.2016-3764","ieee":"G. Mikić, A. Stoll, J. Bevirt, R. Grah, and M. Moore, “Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency,” presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA, 2016, pp. 1–19."},"quality_controlled":"1","title":"Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency","date_created":"2018-12-11T11:50:47Z","year":"2016","publist_id":"6114","date_updated":"2023-02-21T10:17:50Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"status":"public","publication_status":"published","day":"01","month":"06","conference":{"location":"Washington, D.C., USA","end_date":"2016-06-17","start_date":"2016-06-13","name":"AIAA: Aviation Technology, Integration, and Operations Conference"},"language":[{"iso":"eng"}],"date_published":"2016-06-01T00:00:00Z"}]