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Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003.","ama":"Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses. 2017. doi:10.1371/journal.pcbi.1005609.s003","mla":"Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003.","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction for Multiple Stresses.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s003.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Heuristic prediction for multiple stresses. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s003","short":"M. Lukacisinova, S. Novak, T. 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Lukacisinova, S. Novak, T. Paixao, (2017).","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Resistance frequencies for different combination strategies. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s004","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.","mla":"Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004.","ama":"Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004.","ieee":"M. Lukacisinova, S. Novak, and T. 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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."}],"language":[{"iso":"eng"}],"type":"journal_article","author":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","full_name":"Steinrück, Magdalena","first_name":"Magdalena","last_name":"Steinrück","orcid":"0000-0003-1229-9719"},{"orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"publist_id":"6990","date_updated":"2026-11-10T23:30:16Z","scopus_import":"1","date_created":"2018-12-11T11:48:01Z","year":"2017","publication":"eLife","publication_status":"published","file_date_updated":"2020-07-14T12:47:48Z","isi":1,"article_number":"e25100","intvolume":" 6","date_published":"2017-07-25T00:00:00Z","month":"07","ddc":["576"],"publisher":"eLife Sciences Publications","oa_version":"Published Version","citation":{"short":"M. Steinrück, C.C. Guet, ELife 6 (2017).","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.","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.","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","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.","ista":"Steinrück M, Guet CC. 2017. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife. 6, e25100.","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"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection","_id":"704","day":"25","publication_identifier":{"issn":["2050-084X"]},"fulldoi":"https://doi.org/10.7554/eLife.25100","department":[{"_id":"CaGu"}],"oa":1,"doi":"10.7554/eLife.25100","file":[{"content_type":"application/pdf","date_created":"2018-12-12T10:12:54Z","file_id":"4975","file_name":"IST-2017-890-v1+1_elife-25100-v1.pdf","file_size":2092088,"creator":"system","checksum":"6b908b5db9f61f6820ebd7f8fa815571","access_level":"open_access","date_updated":"2020-07-14T12:47:48Z","relation":"main_file"},{"content_type":"application/pdf","date_created":"2018-12-12T10:12:55Z","file_id":"4976","file_size":3428681,"file_name":"IST-2017-890-v1+2_elife-25100-figures-v1.pdf","checksum":"ca21530389b720243552678125fdba35","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:47:48Z","relation":"main_file"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"corr_author":"1","article_processing_charge":"No","external_id":{"isi":["000406183700001"]},"volume":6,"has_accepted_license":"1"},{"fulldoi":"https://doi.org/10.1016/j.devcel.2017.09.014","department":[{"_id":"CaHe"},{"_id":"CaGu"},{"_id":"GaTk"}],"page":"198 - 211","publication_identifier":{"issn":["1534-5807"]},"day":"23","title":"An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate","_id":"735","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"volume":43,"article_processing_charge":"No","external_id":{"isi":["000413443700011"]},"corr_author":"1","issue":"2","doi":"10.1016/j.devcel.2017.09.014","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"I2058","name":"Cell segregation in gastrulation: the role of cell fate specification","_id":"252DD2A6-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-11-10T23:30:20Z","publist_id":"6934","scopus_import":"1","author":[{"orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","full_name":"Barone, Vanessa","first_name":"Vanessa","last_name":"Barone"},{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz","first_name":"Moritz","last_name":"Lang"},{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","first_name":"Gabriel","orcid":"0000-0003-4761-5996"},{"first_name":"Saurabh","last_name":"Pradhan","full_name":"Pradhan, Saurabh"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","first_name":"Shayan","last_name":"Shamipour"},{"first_name":"Keisuke","last_name":"Sako","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075"},{"first_name":"Mateusz K","last_name":"Sikora","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"abstract":[{"lang":"eng","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."}],"related_material":{"record":[{"status":"public","id":"961","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"8350","status":"public"}]},"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","status":"public","oa_version":"None","citation":{"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","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.","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.","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.","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","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.","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."},"date_published":"2017-10-23T00:00:00Z","month":"10","publisher":"Cell Press","isi":1,"intvolume":" 43","publication":"Developmental Cell","date_created":"2018-12-11T11:48:13Z","year":"2017","publication_status":"published"},{"intvolume":" 13","article_number":"e1005609","isi":1,"file_date_updated":"2020-07-14T12:47:46Z","publication_status":"published","year":"2017","publication":"PLoS Computational Biology","date_created":"2018-12-11T11:47:58Z","citation":{"short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","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","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.","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.","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","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.","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."},"oa_version":"Published Version","publisher":"Public Library of Science","ddc":["576"],"month":"07","date_published":"2017-07-18T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"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"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9849"},{"id":"9850","relation":"research_data","status":"public"},{"id":"9851","relation":"research_data","status":"public"},{"relation":"research_data","id":"9852","status":"public"},{"status":"public","relation":"dissertation_contains","id":"6263"}]},"quality_controlled":"1","status":"public","pubrep_id":"894","scopus_import":"1","publist_id":"7004","date_updated":"2026-11-10T23:30:52Z","author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","first_name":"Marta","last_name":"Lukacisinova","orcid":"0000-0002-2519-8004"},{"last_name":"Novak","first_name":"Sebastian","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-824X"},{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"}],"issue":"7","corr_author":"1","file":[{"content_type":"application/pdf","file_id":"5117","date_created":"2018-12-12T10:15:01Z","file_size":3775716,"file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","checksum":"9143c290fa6458ed2563bff4b295554a","creator":"system","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:47:46Z"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"doi":"10.1371/journal.pcbi.1005609","oa":1,"project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7"}],"volume":13,"has_accepted_license":"1","article_type":"original","external_id":{"isi":["000406619800014"]},"article_processing_charge":"No","_id":"696","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"fulldoi":"https://doi.org/10.1371/journal.pcbi.1005609","day":"18","publication_identifier":{"issn":["1553-734X"]}},{"type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"418","status":"public"},{"relation":"part_of_dissertation","id":"7680","status":"public"}]},"quality_controlled":"1","status":"public","scopus_import":"1","publist_id":"6362","date_updated":"2026-11-10T23:30:56Z","author":[{"last_name":"Kainrath","first_name":"Stephanie","full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6709-2195"},{"full_name":"Stadler, Manuela","last_name":"Stadler","first_name":"Manuela"},{"last_name":"Gschaider-Reichhart","first_name":"Eva","full_name":"Gschaider-Reichhart, Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7218-7738"},{"first_name":"Martin","last_name":"Distel","full_name":"Distel, Martin"},{"last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"}],"intvolume":" 56","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)","isi":1,"file_date_updated":"2019-01-18T09:39:55Z","publication_status":"published","date_created":"2018-12-11T11:49:46Z","year":"2017","publication":"Angewandte Chemie International Edition","citation":{"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, 2017. https://doi.org/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, 2017, pp. 4608–11, doi:10.1002/anie.201611998.","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. https://doi.org/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.","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, pp. 4608–4611, 2017.","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.","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"},"oa_version":"Published Version","publisher":"Wiley","ddc":["540"],"month":"03","date_published":"2017-03-20T00:00:00Z","_id":"1028","title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"fulldoi":"https://doi.org/10.1002/anie.201611998","page":"4608-4611","publication_identifier":{"issn":["1433-7851"]},"day":"20","issue":"16","corr_author":"1","file":[{"date_updated":"2019-01-18T09:39:55Z","relation":"main_file","success":1,"access_level":"open_access","creator":"dernst","file_name":"2017_communications_Kainrath.pdf","file_size":2614942,"file_id":"5845","date_created":"2019-01-18T09:39:55Z","content_type":"application/pdf"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa":1,"doi":"10.1002/anie.201611998","project":[{"call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"volume":56,"has_accepted_license":"1","das_tickbox":"1","external_id":{"isi":["000398154000038"]},"article_processing_charge":"No"},{"conference":{"name":"CONCUR: Concurrency Theory","start_date":"2016-08-23","location":"Quebec City; Canada","end_date":"2016-08-26"},"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","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"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"doi":"10.4230/LIPIcs.CONCUR.2016.20","oa":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_updated":"2018-12-12T10:11:39Z","relation":"main_file","access_level":"open_access","creator":"system","file_size":501827,"file_name":"IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf","file_id":"4895","date_created":"2018-12-12T10:11:39Z","content_type":"application/pdf"}],"volume":59,"has_accepted_license":"1","alternative_title":["LIPIcs"],"title":"Linear distances between Markov chains","_id":"1093","ec_funded":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20","department":[{"_id":"ToHe"},{"_id":"KrCh"},{"_id":"CaGu"}],"day":"01","file_date_updated":"2018-12-12T10:11:39Z","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF) under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award), by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced Postdoc. Mobility Fellowship – grant number P300P2_161067.","article_number":"20","intvolume":" 59","year":"2016","date_created":"2018-12-11T11:50:06Z","publication_status":"published","citation":{"ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City; Canada, 2016, vol. 59.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.20","mla":"Daca, Przemyslaw, et al. Linear Distances between Markov Chains. Vol. 59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.20.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Linear distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016."},"oa_version":"Published Version","date_published":"2016-08-01T00:00:00Z","month":"08","ddc":["004"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1155"}]},"abstract":[{"lang":"eng","text":"We introduce a general class of distances (metrics) between Markov chains, which are based on linear behaviour. This class encompasses distances given topologically (such as the total variation distance or trace distance) as well as by temporal logics or automata. We investigate which of the distances can be approximated by observing the systems, i.e. by black-box testing or simulation, and we provide both negative and positive results. "}],"language":[{"iso":"eng"}],"type":"conference","pubrep_id":"794","quality_controlled":"1","status":"public","publist_id":"6283","date_updated":"2026-04-15T10:02:12Z","scopus_import":1,"author":[{"last_name":"Daca","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky","orcid":"0000-0002-8122-2881"},{"orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","first_name":"Tatjana"}]},{"year":"2016","date_created":"2018-12-11T11:50:47Z","doi":"10.2514/6.2016-3764","oa":1,"publication_status":"published","conference":{"name":"AIAA: Aviation Technology, Integration, and Operations Conference","location":"Washington, D.C., USA","start_date":"2016-06-13","end_date":"2016-06-17"},"date_published":"2016-06-01T00:00:00Z","month":"06","publisher":"AIAA","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","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.","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","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.","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.","short":"G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19."},"oa_version":"Preprint","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"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","quality_controlled":"1","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."}],"language":[{"iso":"eng"}],"title":"Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency","type":"conference","_id":"1220","day":"01","page":"1 - 19","author":[{"full_name":"Mikić, Gregor","last_name":"Mikić","first_name":"Gregor"},{"full_name":"Stoll, Alex","last_name":"Stoll","first_name":"Alex"},{"last_name":"Bevirt","first_name":"Joe","full_name":"Bevirt, Joe"},{"first_name":"Rok","last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok","orcid":"0000-0003-2539-3560"},{"first_name":"Mark","last_name":"Moore","full_name":"Moore, Mark"}],"publist_id":"6114","date_updated":"2023-02-21T10:17:50Z","scopus_import":1,"fulldoi":"https://doi.org/10.2514/6.2016-3764","department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"citation":{"mla":"Daca, Przemyslaw, et al. Faster Statistical Model Checking for Unbounded Temporal Properties. Vol. 9636, Springer, 2016, pp. 112–29, doi:10.1007/978-3-662-49674-9_7.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties,” 9636:112–29. Springer, 2016. https://doi.org/10.1007/978-3-662-49674-9_7.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Faster statistical model checking for unbounded temporal properties (Vol. 9636, pp. 112–129). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands: Springer. https://doi.org/10.1007/978-3-662-49674-9_7","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Springer, 2016, pp. 112–129.","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands, 2016, vol. 9636, pp. 112–129.","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Faster statistical model checking for unbounded temporal properties. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9636, 112–129.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. In: Vol 9636. Springer; 2016:112-129. doi:10.1007/978-3-662-49674-9_7"},"oa_version":"Preprint","date_published":"2016-01-01T00:00:00Z","publisher":"Springer","month":"01","intvolume":" 9636","isi":1,"acknowledgement":"This research was funded in part by the European Research Council (ERC) under\r\ngrant agreement 267989 (QUAREM), the Austrian Science Fund (FWF) under\r\ngrants project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Peo-\r\nple Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734, the SNSF Advanced Postdoc.\r\nMobility Fellowship – grant number P300P2\r\n161067, and the Czech Science Foun-\r\ndation under grant agreement P202/12/G061.","publication_status":"published","year":"2016","date_created":"2018-12-11T11:50:51Z","scopus_import":"1","publist_id":"6099","date_updated":"2026-04-15T10:02:12Z","author":[{"last_name":"Daca","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan"},{"orcid":"0000-0002-9041-0905","first_name":"Tatjana","last_name":"Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"471"},{"id":"1155","relation":"dissertation_contains","status":"public"}]},"abstract":[{"text":"We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds.","lang":"eng"}],"type":"conference","quality_controlled":"1","status":"public","volume":9636,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.05739"}],"alternative_title":["LNCS"],"article_processing_charge":"No","external_id":{"isi":["000406428000007"],"arxiv":["1504.05739"]},"conference":{"start_date":"2016-04-02","location":"Eindhoven, The Netherlands","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2016-04-08"},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"doi":"10.1007/978-3-662-49674-9_7","oa":1,"fulldoi":"https://doi.org/10.1007/978-3-662-49674-9_7","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"page":"112 - 129","arxiv":1,"day":"01","title":"Faster statistical model checking for unbounded temporal properties","_id":"1234","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"project":[{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level"}],"doi":"10.1016/j.cub.2015.12.041","issue":"3","article_processing_charge":"No","external_id":{"isi":["000369502900034"]},"volume":26,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Bacterial autoimmunity due to a restriction-modification system","_id":"1243","page":"404 - 409","day":"08","fulldoi":"https://doi.org/10.1016/j.cub.2015.12.041","department":[{"_id":"CaGu"}],"publication":"Current Biology","year":"2016","date_created":"2018-12-11T11:50:54Z","publication_status":"published","acknowledgement":"This work was funded by an HFSP Young Investigators’ grant. M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria. R.O. and Y.W. were supported by the Platform for Dynamic Approaches to Living System from MEXT, Japan. We wish to thank I. Kobayashi for providing us with the EcoRI and EcoRV plasmids, and A. Campbell for providing us with the λ vir phage. We thank D. Siekhaus and C. Uhler and members of the C.C.G. and J.P. Bollback laboratories for in-depth discussions. We thank B. Stern for comments on an earlier version of the manuscript. We especially thank B.R. Levin for advice and comments, and the anonymous reviewers for significantly improving the manuscript.","isi":1,"intvolume":" 26","date_published":"2016-02-08T00:00:00Z","month":"02","publisher":"Cell Press","oa_version":"None","citation":{"mla":"Pleska, Maros, et al. “Bacterial Autoimmunity Due to a Restriction-Modification System.” Current Biology, vol. 26, no. 3, Cell Press, 2016, pp. 404–09, doi:10.1016/j.cub.2015.12.041.","chicago":"Pleska, Maros, Long Qian, Reiko Okura, Tobias Bergmiller, Yuichi Wakamoto, Edo Kussell, and Calin C Guet. “Bacterial Autoimmunity Due to a Restriction-Modification System.” Current Biology. Cell Press, 2016. https://doi.org/10.1016/j.cub.2015.12.041.","apa":"Pleska, M., Qian, L., Okura, R., Bergmiller, T., Wakamoto, Y., Kussell, E., & Guet, C. C. (2016). Bacterial autoimmunity due to a restriction-modification system. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2015.12.041","short":"M. Pleska, L. Qian, R. Okura, T. Bergmiller, Y. Wakamoto, E. Kussell, C.C. Guet, Current Biology 26 (2016) 404–409.","ista":"Pleska M, Qian L, Okura R, Bergmiller T, Wakamoto Y, Kussell E, Guet CC. 2016. Bacterial autoimmunity due to a restriction-modification system. Current Biology. 26(3), 404–409.","ieee":"M. Pleska et al., “Bacterial autoimmunity due to a restriction-modification system,” Current Biology, vol. 26, no. 3. Cell Press, pp. 404–409, 2016.","ama":"Pleska M, Qian L, Okura R, et al. Bacterial autoimmunity due to a restriction-modification system. Current Biology. 2016;26(3):404-409. doi:10.1016/j.cub.2015.12.041"},"status":"public","quality_controlled":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"202"}]},"abstract":[{"text":"Restriction-modification (RM) systems represent a minimal and ubiquitous biological system of self/non-self discrimination in prokaryotes [1], which protects hosts from exogenous DNA [2]. The mechanism is based on the balance between methyltransferase (M) and cognate restriction endonuclease (R). M tags endogenous DNA as self by methylating short specific DNA sequences called restriction sites, whereas R recognizes unmethylated restriction sites as non-self and introduces a double-stranded DNA break [3]. Restriction sites are significantly underrepresented in prokaryotic genomes [4-7], suggesting that the discrimination mechanism is imperfect and occasionally leads to autoimmunity due to self-DNA cleavage (self-restriction) [8]. Furthermore, RM systems can promote DNA recombination [9] and contribute to genetic variation in microbial populations, thus facilitating adaptive evolution [10]. However, cleavage of self-DNA by RM systems as elements shaping prokaryotic genomes has not been directly detected, and its cause, frequency, and outcome are unknown. We quantify self-restriction caused by two RM systems of Escherichia coli and find that, in agreement with levels of restriction site avoidance, EcoRI, but not EcoRV, cleaves self-DNA at a measurable rate. Self-restriction is a stochastic process, which temporarily induces the SOS response, and is followed by DNA repair, maintaining cell viability. We find that RM systems with higher restriction efficiency against bacteriophage infections exhibit a higher rate of self-restriction, and that this rate can be further increased by stochastic imbalance between R and M. Our results identify molecular noise in RM systems as a factor shaping prokaryotic genomes.","lang":"eng"}],"language":[{"iso":"eng"}],"type":"journal_article","author":[{"orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","first_name":"Maros"},{"full_name":"Qian, Long","first_name":"Long","last_name":"Qian"},{"full_name":"Okura, Reiko","first_name":"Reiko","last_name":"Okura"},{"orcid":"0000-0001-5396-4346","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wakamoto, Yuichi","last_name":"Wakamoto","first_name":"Yuichi"},{"full_name":"Kussell, Edo","first_name":"Edo","last_name":"Kussell"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-08T14:19:43Z","publist_id":"6087","scopus_import":"1"},{"type":"journal_article","abstract":[{"text":"In bacteria, replicative aging manifests as a difference in growth or survival between the two cells emerging from division. One cell can be regarded as an aging mother with a decreased potential for future survival and division, the other as a rejuvenated daughter. Here, we aimed at investigating some of the processes involved in aging in the bacterium Escherichia coli, where the two types of cells can be distinguished by the age of their cell poles. We found that certain changes in the regulation of the carbohydrate metabolism can affect aging. A mutation in the carbon storage regulator gene, csrA, leads to a dramatically shorter replicative lifespan; csrA mutants stop dividing once their pole exceeds an age of about five divisions. These old-pole cells accumulate glycogen at their old cell poles; after their last division, they do not contain a chromosome, presumably because of spatial exclusion by the glycogen aggregates. The new-pole daughters produced by these aging mothers are born young; they only express the deleterious phenotype once their pole is old. These results demonstrate how manipulations of nutrient allocation can lead to the exclusion of the chromosome and limit replicative lifespan in E. coli, and illustrate how mutations can have phenotypic effects that are specific for cells with old poles. This raises the question how bacteria can avoid the accumulation of such mutations in their genomes over evolutionary times, and how they can achieve the long replicative lifespans that have recently been reported.","lang":"eng"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9873"}]},"language":[{"iso":"eng"}],"pubrep_id":"705","status":"public","quality_controlled":"1","date_updated":"2025-09-22T09:10:03Z","publist_id":"6077","scopus_import":"1","author":[{"full_name":"Boehm, Alex","last_name":"Boehm","first_name":"Alex"},{"full_name":"Arnoldini, Markus","last_name":"Arnoldini","first_name":"Markus"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346"},{"full_name":"Röösli, Thomas","first_name":"Thomas","last_name":"Röösli"},{"full_name":"Bigosch, Colette","first_name":"Colette","last_name":"Bigosch"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"}],"article_number":"e1005974","acknowledgement":"This manuscript is dedicated to the memory of Alex Böhm, who was a great friend and a passionate biologist. Alex passed away after the initial submission of this manuscript. We thank Vesna Olivera and Ursula Sauder from the Zentrum für Mikroskopie Uni Basel for excellent service, and Olin Silander, Nikki Freed, and Nela Nikolic for helpful discussions. This work was supported by the Swiss National Science Foundation grants to M. Ackermann and Urs Jenal (supporting AB).","isi":1,"intvolume":" 12","file_date_updated":"2020-07-14T12:44:41Z","publication":"PLoS Genetics","date_created":"2018-12-11T11:50:56Z","year":"2016","publication_status":"published","citation":{"ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 2016;12(4). doi:10.1371/journal.pgen.1005974","ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. 12(4), e1005974.","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Genetic manipulation of glycogen allocation affects replicative lifespan in E coli,” PLoS Genetics, vol. 12, no. 4. Public Library of Science, 2016.","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, PLoS Genetics 12 (2016).","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann, M. (2016). Genetic manipulation of glycogen allocation affects replicative lifespan in E coli. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” PLoS Genetics. Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1005974.","mla":"Boehm, Alex, et al. “Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E Coli.” PLoS Genetics, vol. 12, no. 4, e1005974, Public Library of Science, 2016, doi:10.1371/journal.pgen.1005974."},"oa_version":"Published Version","month":"04","ddc":["576","579"],"publisher":"Public Library of Science","date_published":"2016-04-19T00:00:00Z","_id":"1250","title":"Genetic manipulation of glycogen allocation affects replicative lifespan in E coli","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"CaGu"}],"fulldoi":"https://doi.org/10.1371/journal.pgen.1005974","day":"19","issue":"4","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:44:41Z","content_type":"application/pdf","date_created":"2018-12-12T10:14:17Z","file_id":"5067","file_name":"IST-2016-705-v1+1_journal.pgen.1005974.PDF","file_size":6273249,"checksum":"53d22b2b39e5adc243d34f18b2615a85","creator":"system"}],"doi":"10.1371/journal.pgen.1005974","oa":1,"has_accepted_license":"1","volume":12,"external_id":{"isi":["000375231900025"]},"article_processing_charge":"No"},{"issue":"11","oa":1,"doi":"10.1038/nchembio.2176","volume":12,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/","open_access":"1"}],"external_id":{"isi":["000386798800008"]},"article_processing_charge":"No","_id":"1290","title":"Compounds that select against the tetracycline-resistance efflux pump","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"fulldoi":"https://doi.org/10.1038/nchembio.2176","page":"902 - 904","day":"01","intvolume":" 12","isi":1,"acknowledgement":"This work was supported in part by National Institute of Allergy and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to L.K.S.).\r\n","publication_status":"published","year":"2016","date_created":"2018-12-11T11:51:10Z","publication":"Nature Chemical Biology","citation":{"apa":"Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., & Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.2176","chicago":"Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/nchembio.2176.","mla":"Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi:10.1038/nchembio.2176.","short":"L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904.","ama":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 2016;12(11):902-904. doi:10.1038/nchembio.2176","ista":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904.","ieee":"L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” Nature Chemical Biology, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016."},"oa_version":"Preprint","publisher":"Nature Publishing Group","month":"11","date_published":"2016-11-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline."}],"status":"public","quality_controlled":"1","scopus_import":"1","date_updated":"2025-09-22T08:30:48Z","publist_id":"6026","author":[{"first_name":"Laura","last_name":"Stone","full_name":"Stone, Laura"},{"last_name":"Baym","first_name":"Michael","full_name":"Baym, Michael"},{"last_name":"Lieberman","first_name":"Tami","full_name":"Lieberman, Tami"},{"orcid":"0000-0003-0876-3187","first_name":"Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P"},{"last_name":"Clardy","first_name":"Jon","full_name":"Clardy, Jon"},{"first_name":"Roy","last_name":"Kishony","full_name":"Kishony, Roy"}]},{"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"oa":1,"doi":"10.1109/ACC.2016.7526722","file":[{"checksum":"7219432b43defc62a0d45f48d4ce6a19","creator":"system","file_name":"IST-2017-810-v1+1_root.pdf","file_size":539166,"file_id":"5203","date_created":"2018-12-12T10:16:17Z","content_type":"application/pdf","relation":"main_file","date_updated":"2025-06-25T11:46:36Z","access_level":"open_access"}],"conference":{"location":"Boston, MA, USA","start_date":"2016-07-06","name":"ACC: American Control Conference","end_date":"2016-07-08"},"article_processing_charge":"No","volume":"2016-July","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"title":"Scale-invariant systems realize nonlinear differential operators","_id":"1320","day":"28","fulldoi":"https://doi.org/10.1109/ACC.2016.7526722","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publication_status":"published","date_created":"2018-12-11T11:51:21Z","year":"2016","file_date_updated":"2025-06-25T11:46:36Z","article_number":"7526722","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734]. Work supported in part by grants AFOSR FA9550-14-1-0060 and NIH 1R01GM100473.","date_published":"2016-07-28T00:00:00Z","publisher":"IEEE","ddc":["003","621"],"month":"07","oa_version":"Submitted Version","citation":{"mla":"Lang, Moritz, and Eduardo Sontag. Scale-Invariant Systems Realize Nonlinear Differential Operators. Vol. 2016–July, 7526722, IEEE, 2016, doi:10.1109/ACC.2016.7526722.","chicago":"Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear Differential Operators,” Vol. 2016–July. IEEE, 2016. https://doi.org/10.1109/ACC.2016.7526722.","apa":"Lang, M., & Sontag, E. (2016). Scale-invariant systems realize nonlinear differential operators (Vol. 2016–July). Presented at the ACC: American Control Conference, Boston, MA, USA: IEEE. https://doi.org/10.1109/ACC.2016.7526722","short":"M. Lang, E. Sontag, in:, IEEE, 2016.","ieee":"M. Lang and E. Sontag, “Scale-invariant systems realize nonlinear differential operators,” presented at the ACC: American Control Conference, Boston, MA, USA, 2016, vol. 2016–July.","ista":"Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July, 7526722.","ama":"Lang M, Sontag E. Scale-invariant systems realize nonlinear differential operators. In: Vol 2016-July. IEEE; 2016. doi:10.1109/ACC.2016.7526722"},"quality_controlled":"1","status":"public","pubrep_id":"810","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"In recent years, several biomolecular systems have been shown to be scale-invariant (SI), i.e. to show the same output dynamics when exposed to geometrically scaled input signals (u → pu, p > 0) after pre-adaptation to accordingly scaled constant inputs. In this article, we show that SI systems-as well as systems invariant with respect to other input transformations-can realize nonlinear differential operators: when excited by inputs obeying functional forms characteristic for a given class of invariant systems, the systems' outputs converge to constant values directly quantifying the speed of the input."}],"OA_place":"repository","type":"conference","author":[{"first_name":"Moritz","last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"full_name":"Sontag, Eduardo","first_name":"Eduardo","last_name":"Sontag"}],"OA_type":"green","scopus_import":"1","date_updated":"2025-06-25T11:46:37Z","publist_id":"5950"},{"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"fulldoi":"https://doi.org/10.1038/ncomms10333","day":"20","_id":"1332","title":"Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","volume":7,"external_id":{"isi":["000369021700002"]},"article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","date_updated":"2020-07-14T12:44:44Z","access_level":"open_access","creator":"system","checksum":"ef147bcbb8bd37e9079cf3ce06f5815d","file_name":"IST-2016-662-v1+1_ncomms10333.pdf","file_size":1844107,"file_id":"5039","date_created":"2018-12-12T10:13:52Z","content_type":"application/pdf"}],"doi":"10.1038/ncomms10333","oa":1,"publist_id":"5936","date_updated":"2025-09-22T08:22:19Z","scopus_import":"1","author":[{"full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait","first_name":"Remy P","orcid":"0000-0003-0876-3187"},{"full_name":"Palmer, Adam","first_name":"Adam","last_name":"Palmer"},{"full_name":"Yelin, Idan","first_name":"Idan","last_name":"Yelin"},{"first_name":"Roy","last_name":"Kishony","full_name":"Kishony, Roy"}],"type":"journal_article","abstract":[{"text":"Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance.","lang":"eng"}],"language":[{"iso":"eng"}],"pubrep_id":"662","quality_controlled":"1","status":"public","citation":{"ama":"Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 2016;7. doi:10.1038/ncomms10333","ista":"Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7, 10333.","ieee":"R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","short":"R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016).","apa":"Chait, R. P., Palmer, A., Yelin, I., & Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10333","chicago":"Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10333.","mla":"Chait, Remy P., et al. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications, vol. 7, 10333, Nature Publishing Group, 2016, doi:10.1038/ncomms10333."},"oa_version":"Published Version","month":"01","ddc":["570","579"],"publisher":"Nature Publishing Group","date_published":"2016-01-20T00:00:00Z","article_number":"10333","acknowledgement":"This work was partially supported by US National Institutes of Health grant R01-GM081617, Israeli Centers of Research Excellence I-CORE Program ISF Grant No. 152/11, and the European Research Council FP7 ERC Grant 281891.","isi":1,"intvolume":" 7","file_date_updated":"2020-07-14T12:44:44Z","publication":"Nature Communications","year":"2016","date_created":"2018-12-11T11:51:25Z","publication_status":"published"}]