[{"oa_version":"Submitted Version","type":"journal_article","date_updated":"2024-03-25T23:30:09Z","day":"17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","department":[{"_id":"EvBe"}],"doi":"10.1007/978-1-4939-6831-2_1","language":[{"iso":"eng"}],"file":[{"file_id":"5068","date_updated":"2019-10-15T07:47:05Z","access_level":"open_access","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","date_created":"2018-12-12T10:14:18Z","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":840646}],"date_published":"2017-03-17T00:00:00Z","page":"1 - 29","alternative_title":["Methods in Molecular Biology"],"scopus_import":1,"publication_identifier":{"issn":["10643745"]},"year":"2017","citation":{"ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29, 2017.","ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29.","chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer, 2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.","apa":"Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1"},"quality_controlled":"1","author":[{"last_name":"Hurny","first_name":"Andrej","orcid":"0000-0003-3638-1426","full_name":"Hurny, Andrej","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"FWF","_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","name":"Hormone cross-talk drives nutrient dependent plant development"}],"abstract":[{"text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges.","lang":"eng"}],"publication_status":"published","title":"Methodological advances in auxin and cytokinin biology","publication":"Auxins and Cytokinins in Plant Biology","_id":"1024","oa":1,"related_material":{"record":[{"id":"539","relation":"dissertation_contains","status":"public"}]},"ddc":["575"],"file_date_updated":"2019-10-15T07:47:05Z","publisher":"Springer","pubrep_id":"1019","volume":1569,"month":"03","date_created":"2018-12-11T11:49:45Z","status":"public","intvolume":" 1569","publist_id":"6369"},{"day":"02","oa_version":"None","type":"journal_article","date_updated":"2023-09-22T09:26:59Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","department":[{"_id":"CaHe"}],"doi":"10.1038/nature21502","language":[{"iso":"eng"}],"page":"43 - 44","external_id":{"isi":["000395671500025"]},"date_published":"2017-03-02T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["00280836"]},"year":"2017","author":[{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","citation":{"short":"C.-P.J. Heisenberg, Nature 543 (2017) 43–44.","chicago":"Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/nature21502.","ista":"Heisenberg C-PJ. 2017. Cell biology: Stretched divisions. Nature. 543(7643), 43–44.","ieee":"C.-P. J. Heisenberg, “Cell biology: Stretched divisions,” Nature, vol. 543, no. 7643. Nature Publishing Group, pp. 43–44, 2017.","ama":"Heisenberg C-PJ. Cell biology: Stretched divisions. Nature. 2017;543(7643):43-44. doi:10.1038/nature21502","mla":"Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature, vol. 543, no. 7643, Nature Publishing Group, 2017, pp. 43–44, doi:10.1038/nature21502.","apa":"Heisenberg, C.-P. J. (2017). Cell biology: Stretched divisions. Nature. Nature Publishing Group. https://doi.org/10.1038/nature21502"},"abstract":[{"text":"Many organ surfaces are covered by a protective epithelial-cell layer. It emerges that such layers are maintained by cell stretching that triggers cell division mediated by the force-sensitive ion-channel protein Piezo1. See Letter p.118","lang":"eng"}],"publication_status":"published","_id":"1025","publication":"Nature","title":"Cell biology: Stretched divisions","publisher":"Nature Publishing Group","issue":"7643","volume":543,"status":"public","month":"03","date_created":"2018-12-11T11:49:45Z","isi":1,"publist_id":"6367","intvolume":" 543"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.copbio.2017.02.006","department":[{"_id":"HaJa"}],"ec_funded":1,"acknowledgement":"This work was supported by grants of the European Union Seventh Framework Programme (CIG-303564), the Human Frontier Science Program (RGY0084_2012), and the Austrian Science Fund FWF (W1232 MolecularDrugTargets).","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","type":"journal_article","date_updated":"2023-09-22T09:26:06Z","oa_version":"None","publication_identifier":{"issn":["09581669"]},"scopus_import":"1","page":"8 - 14","date_published":"2017-12-01T00:00:00Z","external_id":{"isi":["000418313200003"]},"_id":"1026","publication":"Current Opinion in Biotechnology","title":"Optogenetic methods in drug screening: Technologies and applications","publication_status":"published","abstract":[{"lang":"eng","text":"The optogenetic revolution enabled spatially-precise and temporally-precise control over protein function, signaling pathway activation, and animal behavior with tremendous success in the dissection of signaling networks and neural circuits. Very recently, optogenetic methods have been paired with optical reporters in novel drug screening platforms. In these all-optical platforms, light remotely activated ion channels and kinases thereby obviating the use of electrophysiology or reagents. Consequences were remarkable operational simplicity, throughput, and cost-effectiveness that culminated in the identification of new drug candidates. These blueprints for all-optical assays also revealed potential pitfalls and inspire all-optical variants of other screens, such as those that aim at better understanding dynamic drug action or orphan protein function."}],"project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"},{"name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24"}],"quality_controlled":"1","author":[{"full_name":"Agus, Viviana","first_name":"Viviana","last_name":"Agus"},{"first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"citation":{"apa":"Agus, V., & Janovjak, H. L. (2017). Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.006","mla":"Agus, Viviana, and Harald L. Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” Current Opinion in Biotechnology, vol. 48, Elsevier, 2017, pp. 8–14, doi:10.1016/j.copbio.2017.02.006.","ieee":"V. Agus and H. L. Janovjak, “Optogenetic methods in drug screening: Technologies and applications,” Current Opinion in Biotechnology, vol. 48. Elsevier, pp. 8–14, 2017.","ama":"Agus V, Janovjak HL. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 2017;48:8-14. doi:10.1016/j.copbio.2017.02.006","short":"V. Agus, H.L. Janovjak, Current Opinion in Biotechnology 48 (2017) 8–14.","chicago":"Agus, Viviana, and Harald L Janovjak. “Optogenetic Methods in Drug Screening: Technologies and Applications.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.006.","ista":"Agus V, Janovjak HL. 2017. Optogenetic methods in drug screening: Technologies and applications. Current Opinion in Biotechnology. 48, 8–14."},"year":"2017","publist_id":"6365","isi":1,"intvolume":" 48","status":"public","date_created":"2018-12-11T11:49:45Z","month":"12","volume":48,"publisher":"Elsevier","article_type":"original"},{"volume":46,"pubrep_id":"801","file_date_updated":"2019-01-18T09:57:57Z","article_type":"original","publisher":"Elsevier","intvolume":" 46","publist_id":"6364","isi":1,"date_created":"2018-12-11T11:49:45Z","month":"08","status":"public","citation":{"mla":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology, vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013.","apa":"Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier. https://doi.org/10.1016/j.copbio.2017.02.013","ieee":"M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding of antibiotic resistance evolution,” Current Opinion in Biotechnology, vol. 46. Elsevier, pp. 90–97, 2017.","ama":"Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97. doi:10.1016/j.copbio.2017.02.013","ista":"Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.","short":"M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017) 90–97.","chicago":"Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology. Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013."},"author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","last_name":"Lukacisinova","first_name":"Marta"},{"last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"year":"2017","title":"Toward a quantitative understanding of antibiotic resistance evolution","publication":"Current Opinion in Biotechnology","ddc":["570"],"oa":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6263"}]},"_id":"1027","project":[{"grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth","_id":"25EB3A80-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","abstract":[{"text":"The rising prevalence of antibiotic resistant bacteria is an increasingly serious public health challenge. To address this problem, recent work ranging from clinical studies to theoretical modeling has provided valuable insights into the mechanisms of resistance, its emergence and spread, and ways to counteract it. A deeper understanding of the underlying dynamics of resistance evolution will require a combination of experimental and theoretical expertise from different disciplines and new technology for studying evolution in the laboratory. Here, we review recent advances in the quantitative understanding of the mechanisms and evolution of antibiotic resistance. We focus on key theoretical concepts and new technology that enables well-controlled experiments. We further highlight key challenges that can be met in the near future to ultimately develop effective strategies for combating resistance.","lang":"eng"}],"date_published":"2017-08-01T00:00:00Z","file":[{"success":1,"date_updated":"2019-01-18T09:57:57Z","file_id":"5846","file_name":"2017_CurrentOpinion_Lukaciinova.pdf","access_level":"open_access","relation":"main_file","date_created":"2019-01-18T09:57:57Z","content_type":"application/pdf","creator":"dernst","file_size":858338}],"external_id":{"isi":["000408077400015"]},"page":"90 - 97","scopus_import":"1","article_processing_charge":"Yes (in subscription journal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2024-03-25T23:30:15Z","type":"journal_article","oa_version":"Published Version","day":"01","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","language":[{"iso":"eng"}],"doi":"10.1016/j.copbio.2017.02.013","department":[{"_id":"ToBo"}],"has_accepted_license":"1"},{"acknowledgement":"This work was supported by a grant from the European Union􏰝s 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)","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.1002/anie.201611998","language":[{"iso":"eng"}],"ec_funded":1,"day":"20","oa_version":"Published Version","date_updated":"2024-03-25T23:30:08Z","type":"journal_article","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","publication_identifier":{"issn":["14337851"]},"page":"4608-4611","file":[{"access_level":"open_access","file_name":"2017_communications_Kainrath.pdf","file_id":"5845","date_updated":"2019-01-18T09:39:55Z","success":1,"creator":"dernst","content_type":"application/pdf","file_size":2614942,"date_created":"2019-01-18T09:39:55Z","relation":"main_file"}],"external_id":{"isi":["000398154000038"]},"date_published":"2017-03-20T00:00:00Z","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"}],"publication_status":"published","project":[{"grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets [do not use to be deleted]","grant_number":"W1232-B24"}],"_id":"1028","ddc":["540"],"oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"418"},{"status":"public","relation":"part_of_dissertation","id":"7680"}]},"publication":"Angewandte Chemie - International Edition","title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","year":"2017","tmp":{"image":"/images/cc_by.png","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"},"quality_controlled":"1","author":[{"full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","first_name":"Stephanie"},{"full_name":"Stadler, Manuela","last_name":"Stadler","first_name":"Manuela"},{"last_name":"Gschaider-Reichhart","first_name":"Eva","orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Distel","first_name":"Martin","full_name":"Distel, Martin"},{"last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"}],"citation":{"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.","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","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.","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.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie - International Edition 56 (2017) 4608–4611.","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","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."},"status":"public","month":"03","date_created":"2018-12-11T11:49:46Z","isi":1,"publist_id":"6362","intvolume":" 56","publisher":"Wiley-Blackwell","file_date_updated":"2019-01-18T09:39:55Z","issue":"16","volume":56},{"volume":12,"issue":"3","pubrep_id":"800","publisher":"Public Library of Science","file_date_updated":"2018-12-12T10:09:47Z","publist_id":"6361","isi":1,"intvolume":" 12","status":"public","article_number":"e0174066","date_created":"2018-12-11T11:49:46Z","month":"03","quality_controlled":"1","author":[{"id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","last_name":"Lukacisin","first_name":"Martin"},{"last_name":"Landon","first_name":"Matthieu","full_name":"Landon, Matthieu"},{"last_name":"Jajoo","first_name":"Rishi","full_name":"Jajoo, Rishi"}],"citation":{"mla":"Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:10.1371/journal.pone.0174066.","apa":"Lukacisin, M., Landon, M., & Jajoo, R. (2017). Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0174066","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast,” PLoS One, vol. 12, no. 3. Public Library of Science, 2017.","ama":"Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 2017;12(3). doi:10.1371/journal.pone.0174066","ista":"Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One. 12(3), e0174066.","short":"M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS One. Public Library of Science, 2017. https://doi.org/10.1371/journal.pone.0174066."},"year":"2017","tmp":{"image":"/images/cc_by.png","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"},"oa":1,"related_material":{"record":[{"id":"5556","status":"public","relation":"popular_science"},{"id":"6392","relation":"dissertation_contains","status":"public"}]},"ddc":["570"],"_id":"1029","title":"Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast","publication":"PLoS One","publication_status":"published","abstract":[{"text":"RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.","lang":"eng"}],"date_published":"2017-03-16T00:00:00Z","file":[{"file_name":"IST-2017-800-v1+1_journal.pone.0174066.pdf","access_level":"open_access","date_updated":"2018-12-12T10:09:47Z","file_id":"4772","creator":"system","content_type":"application/pdf","file_size":3429381,"relation":"main_file","date_created":"2018-12-12T10:09:47Z"}],"external_id":{"isi":["000396318300121"]},"publication_identifier":{"issn":["19326203"]},"scopus_import":"1","article_processing_charge":"Yes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"16","date_updated":"2024-03-25T23:30:03Z","type":"journal_article","oa_version":"Published Version","doi":"10.1371/journal.pone.0174066","language":[{"iso":"eng"}],"department":[{"_id":"ToBo"}],"has_accepted_license":"1"},{"year":"2017","tmp":{"image":"/images/cc_by.png","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"},"author":[{"last_name":"Villányi","first_name":"Márton","orcid":"0000-0001-8126-0426","full_name":"Villányi, Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ista":"Villányi M. 2017. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. 3(1).","chicago":"Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken – Werkstattbericht Der IST Austria Library.” Informationspraxis. Verein Informationspraxis , 2017. https://doi.org/10.11588/ip.2017.1.35227.","short":"M. Villányi, Informationspraxis 3 (2017).","ama":"Villányi M. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. 2017;3(1). doi:10.11588/ip.2017.1.35227","ieee":"M. Villányi, “Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library,” Informationspraxis, vol. 3, no. 1. Verein Informationspraxis , 2017.","apa":"Villányi, M. (2017). Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library. Informationspraxis. Verein Informationspraxis . https://doi.org/10.11588/ip.2017.1.35227","mla":"Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken – Werkstattbericht Der IST Austria Library.” Informationspraxis, vol. 3, no. 1, Verein Informationspraxis , 2017, doi:10.11588/ip.2017.1.35227."},"publication_status":"published","abstract":[{"text":"Auf der Suche nach einem Bibliothekssystem entschied sich die Forschungseinrichtung IST Austria im Jahr 2014 für das Open-Source-Produkt Koha. In einem ersten Schritt wurden zunächst Grundfunktionen aktiviert um im Anschluss diverse zusätzliche Tools zum Einsatz zu bringen. Die große Flexibilität des Systems erlaubt maßgeschneiderte Lösungen für unterschiedlichste Institutionen. Trotz Herausforderungen kann die Bibliothek auf eine erfolgreiche Implementierung zurückblicken.","lang":"ger"},{"lang":"eng","text":"IST Austria was looking for a new library system until 2014 when the research institute decided\r\nto implement Koha. The library first activated basic functions of the open-source product and\r\nthen brought additional tools into operation. The high flexibility of the system allows customized\r\nsolutions for different institutions. Although the library faced some challenges, it can now look\r\nback on a successful implementation."}],"oa":1,"ddc":["020"],"_id":"1030","publication":"Informationspraxis","title":"Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library","article_type":"original","publisher":"Verein Informationspraxis ","popular_science":"1","file_date_updated":"2018-12-12T10:08:20Z","volume":3,"issue":"1","pubrep_id":"799","status":"public","date_created":"2018-12-11T11:49:46Z","month":"01","publist_id":"6360","intvolume":" 3","day":"01","type":"journal_article","date_updated":"2023-10-18T07:49:29Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","doi":"10.11588/ip.2017.1.35227","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"E-Lib"}],"date_published":"2017-01-01T00:00:00Z","file":[{"access_level":"open_access","file_name":"IST-2017-799-v1+1_35227-112025-1-PB.pdf","file_id":"4680","date_updated":"2018-12-12T10:08:20Z","file_size":201163,"creator":"system","content_type":"application/pdf","date_created":"2018-12-12T10:08:20Z","relation":"main_file"}],"publication_identifier":{"issn":["2297-3249"]}},{"status":"public","article_number":"30","month":"12","conference":{"end_date":"2018-01-13","name":"POPL: Programming Languages","location":"Los Angeles, CA, United States","start_date":"2018-01-07"},"date_created":"2021-12-05T23:01:48Z","intvolume":" 2","article_type":"original","publisher":"Association for Computing Machinery","file_date_updated":"2021-12-07T08:06:28Z","issue":"POPL","volume":2,"abstract":[{"text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks.","lang":"eng"}],"publication_status":"published","project":[{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"_id":"10416","oa":1,"ddc":["000"],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5455"}]},"title":"Optimal Dyck reachability for data-dependence and Alias analysis","publication":"Proceedings of the ACM on Programming Languages","year":"2017","tmp":{"image":"/images/cc_by.png","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"},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bhavya","last_name":"Choudhary","full_name":"Choudhary, Bhavya"},{"first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","citation":{"mla":"Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118.","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158118","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability for data-dependence and Alias analysis,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158118","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2(POPL), 30.","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017)."},"arxiv":1,"scopus_import":"1","publication_identifier":{"eissn":["2475-1421"]},"file":[{"file_size":460188,"creator":"cchlebak","content_type":"application/pdf","relation":"main_file","date_created":"2021-12-07T08:06:28Z","file_name":"2017_ACMProgLang_Chatterjee.pdf","checksum":"faa3f7b3fe8aab84b50ed805c26a0ee5","access_level":"open_access","success":1,"file_id":"10421","date_updated":"2021-12-07T08:06:28Z"}],"external_id":{"arxiv":["1910.00241"]},"date_published":"2017-12-27T00:00:00Z","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n","has_accepted_license":"1","department":[{"_id":"KrCh"}],"doi":"10.1145/3158118","language":[{"iso":"eng"}],"ec_funded":1,"day":"27","oa_version":"Published Version","type":"journal_article","date_updated":"2023-02-23T12:27:13Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No"},{"quality_controlled":"1","author":[{"first_name":"Marek","last_name":"Chalupa","full_name":"Chalupa, Marek"},{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis"},{"first_name":"Nishant","last_name":"Sinha","full_name":"Sinha, Nishant"},{"first_name":"Kapil","last_name":"Vaidya","full_name":"Vaidya, Kapil"}],"main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3158119","open_access":"1"}],"citation":{"ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2017).","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158119.","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158119","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for Computing Machinery, 2017, doi:10.1145/3158119.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158119"},"year":"2017","oa":1,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5448"},{"id":"5456","status":"public","relation":"earlier_version"}]},"_id":"10417","title":"Data-centric dynamic partial order reduction","publication":"Proceedings of the ACM on Programming Languages","publication_status":"published","abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence."}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"issue":"POPL","volume":2,"article_type":"original","publisher":"Association for Computing Machinery","intvolume":" 2","status":"public","article_number":"31","date_created":"2021-12-05T23:01:49Z","month":"12","conference":{"location":"Los Angeles, CA, United States","start_date":"2018-01-07","end_date":"2018-01-13","name":"POPL: Programming Languages"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","day":"27","type":"journal_article","date_updated":"2023-02-23T12:27:16Z","oa_version":"Published Version","language":[{"iso":"eng"}],"doi":"10.1145/3158119","department":[{"_id":"KrCh"}],"ec_funded":1,"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","date_published":"2017-12-27T00:00:00Z","external_id":{"arxiv":["1610.01188"]},"publication_identifier":{"eissn":["2475-1421"]},"scopus_import":"1","arxiv":1},{"year":"2017","quality_controlled":"1","author":[{"full_name":"Mciver, Annabelle","first_name":"Annabelle","last_name":"Mciver"},{"full_name":"Morgan, Carroll","last_name":"Morgan","first_name":"Carroll"},{"first_name":"Benjamin Lucien","last_name":"Kaminski","full_name":"Kaminski, Benjamin Lucien"},{"full_name":"Katoen, Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","first_name":"Joost P","last_name":"Katoen"}],"citation":{"apa":"Mciver, A., Morgan, C., Kaminski, B. L., & Katoen, J. P. (2017). A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158121","mla":"Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 33, Association for Computing Machinery, 2017, doi:10.1145/3158121.","chicago":"Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost P Katoen. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158121.","short":"A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM on Programming Languages 2 (2017).","ista":"Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33.","ama":"Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure termination. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158121","ieee":"A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule for almost-sure termination,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017."},"main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3158121","open_access":"1"}],"abstract":[{"text":"We present a new proof rule for proving almost-sure termination of probabilistic programs, including those that contain demonic non-determinism. An important question for a probabilistic program is whether the probability mass of all its diverging runs is zero, that is that it terminates \"almost surely\". Proving that can be hard, and this paper presents a new method for doing so. It applies directly to the program's source code, even if the program contains demonic choice. Like others, we use variant functions (a.k.a. \"super-martingales\") that are real-valued and decrease randomly on each loop iteration; but our key innovation is that the amount as well as the probability of the decrease are parametric. We prove the soundness of the new rule, indicate where its applicability goes beyond existing rules, and explain its connection to classical results on denumerable (non-demonic) Markov chains.","lang":"eng"}],"publication_status":"published","_id":"10418","oa":1,"title":"A new proof rule for almost-sure termination","publication":"Proceedings of the ACM on Programming Languages","article_type":"original","publisher":"Association for Computing Machinery","volume":2,"issue":"POPL","article_number":"33","status":"public","month":"12","conference":{"name":"POPL: Programming Languages","end_date":"2018-01-13","location":"Los Angeles, CA, United States","start_date":"2018-01-07"},"date_created":"2021-12-05T23:01:49Z","intvolume":" 2","day":"07","oa_version":"Published Version","type":"journal_article","date_updated":"2021-12-07T08:04:14Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","acknowledgement":"McIver and Morgan are grateful to David Basin and the Information Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during part of which this work began. And thanks particularly to Andreas Lochbihler, who shared with us the probabilistic termination problem that led to it. They acknowledge the support of ARC grant DP140101119. Part of this work was carried out during the Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden. Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4.","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"doi":"10.1145/3158121","language":[{"iso":"eng"}],"external_id":{"arxiv":["1711.03588"]},"date_published":"2017-12-07T00:00:00Z","arxiv":1,"scopus_import":"1","publication_identifier":{"eissn":["2475-1421"]}},{"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"publication_status":"published","abstract":[{"text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations.","lang":"eng"}],"publication":"Evolution","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","oa":1,"_id":"1063","year":"2017","citation":{"chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.","short":"H. Uecker, Evolution 71 (2017) 845–858.","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191","apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:10.1111/evo.13191."},"main_file_link":[{"url":"http://biorxiv.org/content/early/2016/10/14/081042","open_access":"1"}],"author":[{"last_name":"Uecker","first_name":"Hildegard","full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","date_created":"2018-12-11T11:49:57Z","month":"04","status":"public","intvolume":" 71","publist_id":"6327","isi":1,"publisher":"Wiley-Blackwell","issue":"4","volume":71,"ec_funded":1,"doi":"10.1111/evo.13191","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"type":"journal_article","date_updated":"2025-05-28T11:42:51Z","oa_version":"Submitted Version","day":"01","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["00143820"]},"scopus_import":"1","date_published":"2017-04-01T00:00:00Z","external_id":{"isi":["000398545200003"]},"page":"845 - 858"},{"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"publication_status":"published","abstract":[{"lang":"eng","text":"We consider the problem of reachability in pushdown graphs. We study the problem for pushdown graphs with constant treewidth. Even for pushdown graphs with treewidth 1, for the reachability problem we establish the following: (i) the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem would contradict the k-clique conjecture and imply faster combinatorial algorithms for cliques in graphs."}],"title":"Pushdown reachability with constant treewidth","publication":"Information Processing Letters","ddc":["000"],"oa":1,"_id":"1065","year":"2017","citation":{"apa":"Chatterjee, K., & Osang, G. F. (2017). Pushdown reachability with constant treewidth. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2017.02.003","mla":"Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters, vol. 122, Elsevier, 2017, pp. 25–29, doi:10.1016/j.ipl.2017.02.003.","ama":"Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. Information Processing Letters. 2017;122:25-29. doi:10.1016/j.ipl.2017.02.003","ieee":"K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,” Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017.","short":"K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.","chicago":"Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with Constant Treewidth.” Information Processing Letters. Elsevier, 2017. https://doi.org/10.1016/j.ipl.2017.02.003.","ista":"Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth. Information Processing Letters. 122, 25–29."},"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","last_name":"Osang","first_name":"Georg F"}],"quality_controlled":"1","date_created":"2018-12-11T11:49:57Z","month":"06","status":"public","intvolume":" 122","publist_id":"6323","isi":1,"file_date_updated":"2019-10-15T07:44:51Z","publisher":"Elsevier","volume":122,"pubrep_id":"991","ec_funded":1,"doi":"10.1016/j.ipl.2017.02.003","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"KrCh"},{"_id":"HeEd"}],"date_updated":"2023-09-20T12:08:18Z","type":"journal_article","oa_version":"Submitted Version","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","publication_identifier":{"issn":["00200190"]},"scopus_import":"1","date_published":"2017-06-01T00:00:00Z","file":[{"file_name":"IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf","access_level":"open_access","file_id":"4998","date_updated":"2019-10-15T07:44:51Z","creator":"system","content_type":"application/pdf","file_size":247657,"relation":"main_file","date_created":"2018-12-12T10:13:17Z"}],"external_id":{"isi":["000399506600005"]},"page":"25 - 29"},{"scopus_import":"1","page":"143 - 166","date_published":"2017-06-01T00:00:00Z","external_id":{"isi":["000402025600002"]},"doi":"10.1016/j.ic.2016.10.006","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ec_funded":1,"day":"01","date_updated":"2023-09-20T12:07:48Z","type":"journal_article","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","status":"public","date_created":"2018-12-11T11:49:58Z","month":"06","publist_id":"6322","isi":1,"intvolume":" 254","publisher":"Elsevier","issue":"2","volume":254,"publication_status":"published","abstract":[{"lang":"eng","text":"Simulation is an attractive alternative to language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. While fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable in general, whereas the (quantitative) simulation reduces to quantitative games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games, yet they still admit pseudo-polynomial time algorithms."}],"project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"id":"5428","relation":"earlier_version","status":"public"}]},"_id":"1066","title":"Quantitative fair simulation games","publication":"Information and Computation","year":"2017","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Otop","first_name":"Jan","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"quality_controlled":"1","citation":{"apa":"Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2017). Quantitative fair simulation games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.006","mla":"Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” Information and Computation, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:10.1016/j.ic.2016.10.006.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. “Quantitative Fair Simulation Games.” Information and Computation. Elsevier, 2017. https://doi.org/10.1016/j.ic.2016.10.006.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation 254 (2017) 143–166.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation games. Information and Computation. 254(2), 143–166.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair simulation games,” Information and Computation, vol. 254, no. 2. Elsevier, pp. 143–166, 2017.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation games. Information and Computation. 2017;254(2):143-166. doi:10.1016/j.ic.2016.10.006"}},{"external_id":{"isi":["000395368300007"]},"file":[{"content_type":"application/pdf","creator":"system","file_size":6866187,"date_created":"2018-12-12T10:10:57Z","relation":"main_file","access_level":"open_access","file_name":"IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf","date_updated":"2018-12-12T10:10:57Z","file_id":"4849"}],"date_published":"2017-02-27T00:00:00Z","page":"354 - 366","scopus_import":"1","publication_identifier":{"issn":["15345807"]},"oa_version":"Published Version","date_updated":"2023-09-20T12:06:27Z","type":"journal_article","day":"27","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"acknowledged_ssus":[{"_id":"PreCl"}],"has_accepted_license":"1","department":[{"_id":"CaHe"}],"doi":"10.1016/j.devcel.2017.01.010","language":[{"iso":"eng"}],"file_date_updated":"2018-12-12T10:10:57Z","publisher":"Cell Press","pubrep_id":"869","issue":"4","volume":40,"month":"02","date_created":"2018-12-11T11:49:58Z","status":"public","intvolume":" 40","isi":1,"publist_id":"6320","tmp":{"image":"/images/cc_by.png","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"},"year":"2017","citation":{"chicago":"Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.01.010.","short":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg, Developmental Cell 40 (2017) 354–366.","ista":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 40(4), 354–366.","ama":"Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. 2017;40(4):354-366. doi:10.1016/j.devcel.2017.01.010","ieee":"H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg, “The physical basis of coordinated tissue spreading in zebrafish gastrulation,” Developmental Cell, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.","apa":"Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., & Heisenberg, C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.01.010","mla":"Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading in Zebrafish Gastrulation.” Developmental Cell, vol. 40, no. 4, Cell Press, 2017, pp. 354–66, doi:10.1016/j.devcel.2017.01.010."},"author":[{"last_name":"Morita","first_name":"Hitoshi","full_name":"Morita, Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grigolon, Silvia","last_name":"Grigolon","first_name":"Silvia"},{"first_name":"Martin","last_name":"Bock","full_name":"Bock, Martin"},{"full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel","last_name":"Krens"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"quality_controlled":"1","project":[{"_id":"2524F500-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","grant_number":"201439"}],"abstract":[{"text":"Embryo morphogenesis relies on highly coordinated movements of different tissues. However, remarkably little is known about how tissues coordinate their movements to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements first become apparent during “doming,” when the blastoderm begins to spread over the yolk sac, a process involving coordinated epithelial surface cell layer expansion and mesenchymal deep cell intercalations. Here, we find that active surface cell expansion represents the key process coordinating tissue movements during doming. By using a combination of theory and experiments, we show that epithelial surface cells not only trigger blastoderm expansion by reducing tissue surface tension, but also drive blastoderm thinning by inducing tissue contraction through radial deep cell intercalations. Thus, coordinated tissue expansion and thinning during doming relies on surface cells simultaneously controlling tissue surface tension and radial tissue contraction.","lang":"eng"}],"publication_status":"published","publication":"Developmental Cell","title":"The physical basis of coordinated tissue spreading in zebrafish gastrulation","_id":"1067","oa":1,"ddc":["572","597"]},{"abstract":[{"lang":"eng","text":"Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field."}],"publication_status":"published","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493"}],"_id":"1072","oa":1,"publication":"Transactions of the American Mathematical Society","title":"The Morse theory of Čech and delaunay complexes","year":"2017","quality_controlled":"1","author":[{"id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","last_name":"Bauer","first_name":"Ulrich"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1312.1231"}],"citation":{"ama":"Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 2017;369(5):3741-3762. doi:10.1090/tran/6991","ieee":"U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,” Transactions of the American Mathematical Society, vol. 369, no. 5. American Mathematical Society, pp. 3741–3762, 2017.","short":"U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society 369 (2017) 3741–3762.","chicago":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” Transactions of the American Mathematical Society. American Mathematical Society, 2017. https://doi.org/10.1090/tran/6991.","ista":"Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. 369(5), 3741–3762.","apa":"Bauer, U., & Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay complexes. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/6991","mla":"Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay Complexes.” Transactions of the American Mathematical Society, vol. 369, no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:10.1090/tran/6991."},"status":"public","month":"05","date_created":"2018-12-11T11:49:59Z","isi":1,"publist_id":"6311","intvolume":" 369","publisher":"American Mathematical Society","article_type":"original","volume":369,"issue":"5","acknowledgement":"This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP), by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR 109 “Discretization in Geometry and Dynamics”.","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"doi":"10.1090/tran/6991","ec_funded":1,"day":"01","oa_version":"Preprint","date_updated":"2023-09-20T12:05:56Z","type":"journal_article","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","arxiv":1,"scopus_import":"1","page":"3741 - 3762","external_id":{"isi":["000398030400024"],"arxiv":["1312.1231"]},"date_published":"2017-05-01T00:00:00Z"},{"citation":{"short":"M. Čadek, M. Krcál, L. Vokřínek, Discrete & Computational Geometry 54 (2017) 915–965.","chicago":"Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability of the Lifting Extension Problem.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-016-9855-6.","ista":"Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. 54(4), 915–965.","ieee":"M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting extension problem,” Discrete & Computational Geometry, vol. 54, no. 4. Springer, pp. 915–965, 2017.","ama":"Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. 2017;54(4):915-965. doi:10.1007/s00454-016-9855-6","apa":"Čadek, M., Krcál, M., & Vokřínek, L. (2017). Algorithmic solvability of the lifting extension problem. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-016-9855-6","mla":"Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.” Discrete & Computational Geometry, vol. 54, no. 4, Springer, 2017, pp. 915–65, doi:10.1007/s00454-016-9855-6."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1307.6444"}],"author":[{"full_name":"Čadek, Martin","first_name":"Martin","last_name":"Čadek"},{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek","last_name":"Krcál","first_name":"Marek"},{"last_name":"Vokřínek","first_name":"Lukáš","full_name":"Vokřínek, Lukáš"}],"quality_controlled":"1","year":"2017","title":"Algorithmic solvability of the lifting extension problem","publication":"Discrete & Computational Geometry","_id":"1073","oa":1,"abstract":[{"lang":"eng","text":"Let X and Y be finite simplicial sets (e.g. finite simplicial complexes), both equipped with a free simplicial action of a finite group G. Assuming that Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|; the existence of such a map can be decided even for dimX≤2d+1. This yields the first algorithm for deciding topological embeddability of a k-dimensional finite simplicial complex into Rn under the condition k≤23n−1. More generally, we present an algorithm that, given a lifting-extension problem satisfying an appropriate stability assumption, computes the set of all homotopy classes of solutions. This result is new even in the non-equivariant situation."}],"publication_status":"published","issue":"4","volume":54,"publisher":"Springer","intvolume":" 54","isi":1,"publist_id":"6309","month":"06","date_created":"2018-12-11T11:50:00Z","status":"public","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","date_updated":"2023-09-20T12:01:28Z","type":"journal_article","day":"01","department":[{"_id":"UlWa"}],"doi":"10.1007/s00454-016-9855-6","language":[{"iso":"eng"}],"external_id":{"isi":["000400072700008"]},"date_published":"2017-06-01T00:00:00Z","page":"915 - 965","scopus_import":"1","publication_identifier":{"issn":["01795376"]}},{"related_material":{"record":[{"id":"200","relation":"dissertation_contains","status":"public"}]},"oa":1,"_id":"1074","title":"Inferring recent demography from isolation by distance of long shared sequence blocks","publication":"Genetics","publication_status":"published","abstract":[{"text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance.","lang":"eng"}],"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"author":[{"last_name":"Ringbauer","first_name":"Harald","orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Graham","last_name":"Coop","full_name":"Coop, Graham"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"quality_controlled":"1","citation":{"ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.","chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351. doi:10.1534/genetics.116.196220","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” Genetics, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.","apa":"Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.196220"},"main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/early/2016/09/23/076810"}],"year":"2017","publist_id":"6307","isi":1,"intvolume":" 205","status":"public","date_created":"2018-12-11T11:50:00Z","month":"03","volume":205,"issue":"3","publisher":"Genetics Society of America","doi":"10.1534/genetics.116.196220","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"01","type":"journal_article","date_updated":"2025-05-28T11:42:51Z","oa_version":"Preprint","publication_identifier":{"issn":["00166731"]},"scopus_import":"1","page":"1335 - 1351","date_published":"2017-03-01T00:00:00Z","external_id":{"isi":["000395807200023"]}},{"year":"2017","citation":{"chicago":"Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan, and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.023403.","short":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel, Physical Review A - Atomic, Molecular, and Optical Physics 95 (2017).","ista":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. Physical Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403.","ama":"Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. Physical Review A - Atomic, Molecular, and Optical Physics. 2017;95(2). doi:10.1103/PhysRevA.95.023403","ieee":"M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field ionization via a high-order Coulomb-corrected strong-field approximation,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2. American Physical Society, 2017.","mla":"Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:10.1103/PhysRevA.95.023403.","apa":"Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., & Keitel, C. (2017). Strong-field ionization via a high-order Coulomb-corrected strong-field approximation. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.95.023403"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.07018"}],"quality_controlled":"1","author":[{"full_name":"Klaiber, Michael","first_name":"Michael","last_name":"Klaiber"},{"first_name":"Jiří","last_name":"Daněk","full_name":"Daněk, Jiří"},{"first_name":"Enderalp","last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karen","last_name":"Hatsagortsyan","full_name":"Hatsagortsyan, Karen"},{"last_name":"Keitel","first_name":"Christoph","full_name":"Keitel, Christoph"}],"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"publication_status":"published","abstract":[{"text":"Signatures of the Coulomb corrections in the photoelectron momentum distribution during laser-induced ionization of atoms or ions in tunneling and multiphoton regimes are investigated analytically in the case of a one-dimensional problem. A high-order Coulomb-corrected strong-field approximation is applied, where the exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov state including the second-order corrections to the eikonal. Although without high-order corrections our theory coincides with the known analytical R-matrix (ARM) theory, we propose a simplified procedure for the matrix element derivation. Rather than matching the eikonal Coulomb-Volkov wave function with the bound state as in the ARM theory to remove the Coulomb singularity, we calculate the matrix element via the saddle-point integration method by time as well as by coordinate, and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron momentum distribution with respect to the ARM theory due to high-order corrections is analyzed for tunneling and multiphoton regimes. The relation of the quantum corrections to the tunneling delay time is discussed.","lang":"eng"}],"title":"Strong-field ionization via a high-order Coulomb-corrected strong-field approximation","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","oa":1,"_id":"1076","publisher":"American Physical Society","volume":95,"issue":"2","date_created":"2018-12-11T11:50:01Z","month":"02","article_number":"023403","status":"public","intvolume":" 95","publist_id":"6305","isi":1,"date_updated":"2023-09-20T11:57:23Z","type":"journal_article","oa_version":"Submitted Version","day":"01","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.95.023403","department":[{"_id":"MiLe"}],"date_published":"2017-02-01T00:00:00Z","external_id":{"isi":["000400571700011"]},"publication_identifier":{"issn":["24699926"]},"scopus_import":"1"},{"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"doi":"10.1098/rsif.2016.0139","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"04","oa_version":"Published Version","type":"journal_article","date_updated":"2025-05-28T11:42:51Z","scopus_import":"1","publication_identifier":{"issn":["17425689"]},"file":[{"creator":"dernst","content_type":"application/pdf","file_size":1092015,"date_created":"2019-01-18T09:14:02Z","relation":"main_file","access_level":"open_access","file_name":"2017_JRSI_Redondo.pdf","file_id":"5843","date_updated":"2019-01-18T09:14:02Z","success":1}],"external_id":{"isi":["000393380400001"]},"date_published":"2017-01-04T00:00:00Z","_id":"1077","related_material":{"record":[{"status":"public","relation":"research_data","id":"9864"}]},"ddc":["570"],"oa":1,"publication":"Journal of the Royal Society Interface","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"publication_status":"published","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"}],"quality_controlled":"1","author":[{"first_name":"Rodrigo A","last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"Vladar"},{"last_name":"Włodarski","first_name":"Tomasz","full_name":"Włodarski, Tomasz"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"citation":{"apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2016.0139","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:10.1098/rsif.2016.0139.","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” Journal of the Royal Society Interface, vol. 14, no. 126. Royal Society of London, 2017.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface. Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139."},"year":"2017","tmp":{"image":"/images/cc_by.png","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"},"isi":1,"publist_id":"6303","intvolume":" 14","article_number":"20160139","status":"public","month":"01","date_created":"2018-12-11T11:50:01Z","issue":"126","volume":14,"publisher":"Royal Society of London","file_date_updated":"2019-01-18T09:14:02Z"},{"publication":"Journal of visualized experiments JoVE","title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5565"}]},"ddc":["580"],"oa":1,"_id":"1078","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"publication_status":"published","abstract":[{"text":"One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. ","lang":"eng"}],"citation":{"short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017).","chicago":"Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE. Journal of Visualized Experiments, 2017. https://doi.org/10.3791/55044.","ista":"von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017(119), e55044.","ieee":"D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy of plant roots growing on the surface of a gel,” Journal of visualized experiments JoVE, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.","ama":"von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of visualized experiments JoVE. 2017;2017(119). doi:10.3791/55044","mla":"von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE, vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:10.3791/55044.","apa":"von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light sheet fluorescence microscopy of plant roots growing on the surface of a gel. Journal of Visualized Experiments JoVE. Journal of Visualized Experiments. https://doi.org/10.3791/55044"},"author":[{"first_name":"Daniel","last_name":"Von Wangenheim","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","full_name":"Von Wangenheim, Daniel"},{"last_name":"Hauschild","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"year":"2017","intvolume":" 2017","publist_id":"6302","isi":1,"date_created":"2018-12-11T11:50:01Z","month":"01","article_number":"e55044","status":"public","volume":2017,"issue":"119","pubrep_id":"808","file_date_updated":"2018-12-12T10:16:32Z","publisher":"Journal of Visualized Experiments","ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"doi":"10.3791/55044","language":[{"iso":"eng"}],"has_accepted_license":"1","department":[{"_id":"JiFr"},{"_id":"Bio"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","type":"journal_article","date_updated":"2025-05-07T11:12:33Z","oa_version":"Published Version","day":"18","scopus_import":"1","date_published":"2017-01-18T00:00:00Z","file":[{"date_created":"2018-12-12T10:16:31Z","relation":"main_file","file_size":57678,"creator":"system","content_type":"application/pdf","file_id":"5219","date_updated":"2018-12-12T10:16:31Z","access_level":"open_access","file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf"},{"file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","access_level":"open_access","date_updated":"2018-12-12T10:16:32Z","file_id":"5220","file_size":1317820,"creator":"system","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:16:32Z"}],"external_id":{"isi":["000397847200041"]}}]