[{"related_material":{"record":[{"relation":"research_data","id":"9864","status":"public"}]},"date_updated":"2025-05-28T11:42:51Z","citation":{"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.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","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","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.","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.","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","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."},"day":"04","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":1092015,"creator":"dernst","relation":"main_file","file_id":"5843","date_created":"2019-01-18T09:14:02Z","date_updated":"2019-01-18T09:14:02Z","success":1,"file_name":"2017_JRSI_Redondo.pdf"}],"volume":14,"has_accepted_license":"1","month":"01","date_published":"2017-01-04T00:00:00Z","date_created":"2018-12-11T11:50:01Z","issue":"126","publication":"Journal of the Royal Society Interface","intvolume":" 14","quality_controlled":"1","publisher":"Royal Society of London","status":"public","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","article_number":"20160139","author":[{"first_name":"Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A"},{"first_name":"Harold","last_name":"Vladar","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"Vladar, Harold"},{"full_name":"Włodarski, Tomasz","first_name":"Tomasz","last_name":"Włodarski"},{"full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback"}],"oa":1,"isi":1,"year":"2017","type":"journal_article","scopus_import":"1","publist_id":"6303","doi":"10.1098/rsif.2016.0139","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_version":"Published Version","_id":"1077","language":[{"iso":"eng"}],"ddc":["570"],"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer"}],"external_id":{"isi":["000393380400001"]},"ec_funded":1,"abstract":[{"lang":"eng","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."}],"article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2019-01-18T09:14:02Z","publication_identifier":{"issn":["17425689"]}},{"language":[{"iso":"eng"}],"_id":"1078","ddc":["580"],"publication_status":"published","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"external_id":{"isi":["000397847200041"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"},{"_id":"Bio"}],"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"}],"ec_funded":1,"file_date_updated":"2018-12-12T10:16:32Z","article_processing_charge":"No","year":"2017","isi":1,"type":"journal_article","scopus_import":"1","pubrep_id":"808","doi":"10.3791/55044","publist_id":"6302","oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"Bio"}],"issue":"119","publisher":"Journal of Visualized Experiments","publication":"Journal of visualized experiments JoVE","intvolume":" 2017","title":"Light sheet fluorescence microscopy of plant roots growing on the surface of a gel","article_number":"e55044","status":"public","oa":1,"author":[{"full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","last_name":"Von Wangenheim","orcid":"0000-0002-6862-1247","first_name":"Daniel"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"}],"related_material":{"record":[{"relation":"popular_science","id":"5565","status":"public"}]},"citation":{"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","short":"D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments JoVE 2017 (2017).","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.","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.","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","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.","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."},"day":"18","file":[{"file_name":"IST-2017-808-v1+1_2017_VWangenheim_list.pdf","date_updated":"2018-12-12T10:16:31Z","date_created":"2018-12-12T10:16:31Z","file_id":"5219","creator":"system","relation":"main_file","file_size":57678,"access_level":"open_access","content_type":"application/pdf"},{"date_created":"2018-12-12T10:16:32Z","file_size":1317820,"relation":"main_file","file_id":"5220","creator":"system","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-808-v1+2_2017_VWangenheim_article.pdf","date_updated":"2018-12-12T10:16:32Z"}],"date_updated":"2025-05-07T11:12:33Z","has_accepted_license":"1","volume":2017,"date_published":"2017-01-18T00:00:00Z","date_created":"2018-12-11T11:50:01Z","month":"01"},{"citation":{"short":"P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017).","apa":"Nam, P., & Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-017-9238-0","ieee":"P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2. Springer, 2017.","ama":"Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 2017;20(2). doi:10.1007/s11040-017-9238-0","ista":"Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 20(2), 6.","mla":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2, 6, Springer, 2017, doi:10.1007/s11040-017-9238-0.","chicago":"Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis and Geometry. Springer, 2017. https://doi.org/10.1007/s11040-017-9238-0."},"day":"01","date_updated":"2023-09-20T11:53:35Z","volume":20,"date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:50:02Z","month":"06","issue":"2","main_file_link":[{"url":"https://arxiv.org/abs/1603.07368","open_access":"1"}],"quality_controlled":"1","publisher":"Springer","publication":"Mathematical Physics, Analysis and Geometry","intvolume":" 20","title":"Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges","article_number":"6","status":"public","oa":1,"author":[{"first_name":"Phan","last_name":"Nam","full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van Den Bosch, Hanne","first_name":"Hanne","last_name":"Van Den Bosch"}],"type":"journal_article","year":"2017","isi":1,"scopus_import":"1","publist_id":"6300","doi":"10.1007/s11040-017-9238-0","oa_version":"Submitted Version","_id":"1079","language":[{"iso":"eng"}],"publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"external_id":{"isi":["000401270000004"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"RoSe"}],"abstract":[{"lang":"eng","text":"We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory for atoms and molecules. We prove the nonexistence of minimizers for the energy functional when the number of electrons is large and the total nuclear charge is small. This nonexistence result also applies to external potentials decaying faster than the Coulomb potential. In the case of arbitrary nuclear charges, we obtain the nonexistence of stable minimizers and radial minimizers."}],"publication_identifier":{"issn":["13850172"]},"article_processing_charge":"No"},{"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5133","creator":"system","file_size":897050,"date_created":"2018-12-12T10:15:15Z","date_updated":"2018-12-12T10:15:15Z","file_name":"IST-2017-786-v1+1_ncomms14114.pdf"}],"citation":{"chicago":"Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14114.","mla":"Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications, vol. 8, 14114, Nature Publishing Group, 2017, doi:10.1038/ncomms14114.","ama":"Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 2017;8. doi:10.1038/ncomms14114","ista":"Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114.","ieee":"J. Reiter et al., “Reconstructing metastatic seeding patterns of human cancers,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","short":"J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017).","apa":"Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14114"},"day":"31","date_updated":"2023-09-20T11:55:31Z","date_published":"2017-01-31T00:00:00Z","date_created":"2018-12-11T11:50:02Z","month":"01","has_accepted_license":"1","volume":8,"publisher":"Nature Publishing Group","quality_controlled":"1","intvolume":" 8","publication":"Nature Communications","oa":1,"author":[{"first_name":"Johannes","orcid":"0000-0002-0170-7353","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes"},{"full_name":"Makohon Moore, Alvin","first_name":"Alvin","last_name":"Makohon Moore"},{"first_name":"Jeffrey","last_name":"Gerold","full_name":"Gerold, Jeffrey"},{"full_name":"Božić, Ivana","first_name":"Ivana","last_name":"Božić"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Iacobuzio Donahue, Christine","last_name":"Iacobuzio Donahue","first_name":"Christine"},{"last_name":"Vogelstein","first_name":"Bert","full_name":"Vogelstein, Bert"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"article_number":"14114","title":"Reconstructing metastatic seeding patterns of human cancers","status":"public","pubrep_id":"786","scopus_import":"1","isi":1,"year":"2017","type":"journal_article","oa_version":"Published Version","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"},"doi":"10.1038/ncomms14114","publist_id":"6301","external_id":{"isi":["000393096600001"]},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"}],"department":[{"_id":"KrCh"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","ddc":["004","006"],"language":[{"iso":"eng"}],"_id":"1080","publication_identifier":{"issn":["20411723"]},"file_date_updated":"2018-12-12T10:15:15Z","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods."}],"ec_funded":1},{"abstract":[{"lang":"eng","text":"BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities."}],"publication_identifier":{"issn":[" 0950382X"]},"article_processing_charge":"No","publication_status":"published","_id":"1084","language":[{"iso":"eng"}],"external_id":{"isi":["000398059200002"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"CaGu"}],"publist_id":"6294","doi":"10.1111/mmi.13597","oa_version":"None","scopus_import":"1","year":"2017","type":"journal_article","isi":1,"title":"Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis","status":"public","author":[{"full_name":"Fang, Chong","last_name":"Fang","first_name":"Chong"},{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","full_name":"Nagy-Staron, Anna A","last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","first_name":"Anna A"},{"last_name":"Grafe","first_name":"Martin","full_name":"Grafe, Martin"},{"full_name":"Heermann, Ralf","first_name":"Ralf","last_name":"Heermann"},{"last_name":"Jung","first_name":"Kirsten","full_name":"Jung, Kirsten"},{"full_name":"Gebhard, Susanne","first_name":"Susanne","last_name":"Gebhard"},{"last_name":"Mascher","first_name":"Thorsten","full_name":"Mascher, Thorsten"}],"issue":"1","publisher":"Wiley-Blackwell","quality_controlled":"1","page":"16 - 31","intvolume":" 104","publication":"Molecular Microbiology","volume":104,"date_created":"2018-12-11T11:50:03Z","date_published":"2017-04-01T00:00:00Z","month":"04","day":"01","citation":{"chicago":"Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology. Wiley-Blackwell, 2017. https://doi.org/10.1111/mmi.13597.","ama":"Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 2017;104(1):16-31. doi:10.1111/mmi.13597","ista":"Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31.","mla":"Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:10.1111/mmi.13597.","apa":"Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., & Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.13597","short":"C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31.","ieee":"C. Fang et al., “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” Molecular Microbiology, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017."},"date_updated":"2023-09-20T11:48:43Z"},{"quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Nature Communications","intvolume":" 8","title":"Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation","article_number":"14251","status":"public","oa":1,"author":[{"first_name":"Alison","last_name":"Wright","full_name":"Wright, Alison"},{"first_name":"Iulia","last_name":"Darolti","full_name":"Darolti, Iulia"},{"last_name":"Bloch","first_name":"Natasha","full_name":"Bloch, Natasha"},{"last_name":"Oostra","first_name":"Vicencio","full_name":"Oostra, Vicencio"},{"last_name":"Sandkam","first_name":"Benjamin","full_name":"Sandkam, Benjamin"},{"last_name":"Buechel","first_name":"Séverine","full_name":"Buechel, Séverine"},{"full_name":"Kolm, Niclas","last_name":"Kolm","first_name":"Niclas"},{"last_name":"Breden","first_name":"Felix","full_name":"Breden, Felix"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"},{"full_name":"Mank, Judith","first_name":"Judith","last_name":"Mank"}],"day":"31","citation":{"ieee":"A. Wright et al., “Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","apa":"Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., … Mank, J. (2017). Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14251","short":"A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm, F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017).","chicago":"Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14251.","mla":"Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications, vol. 8, 14251, Nature Publishing Group, 2017, doi:10.1038/ncomms14251.","ista":"Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 8, 14251.","ama":"Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 2017;8. doi:10.1038/ncomms14251"},"file":[{"file_id":"5141","creator":"system","relation":"main_file","file_size":955256,"date_created":"2018-12-12T10:15:22Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2018-12-12T10:15:22Z","file_name":"IST-2017-791-v1+1_ncomms14251.pdf"}],"date_updated":"2023-09-20T11:48:16Z","has_accepted_license":"1","volume":8,"date_published":"2017-01-31T00:00:00Z","date_created":"2018-12-11T11:50:04Z","month":"01","_id":"1085","language":[{"iso":"eng"}],"publication_status":"published","ddc":["570","576"],"external_id":{"isi":["000392953700001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"BeVi"}],"abstract":[{"lang":"eng","text":"Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution."}],"file_date_updated":"2018-12-12T10:15:22Z","publication_identifier":{"issn":["20411723"]},"article_processing_charge":"No","isi":1,"type":"journal_article","year":"2017","scopus_import":"1","pubrep_id":"791","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"},"publist_id":"6292","doi":"10.1038/ncomms14251","oa_version":"Published Version"},{"article_processing_charge":"No","publication_identifier":{"issn":["00221120"]},"ec_funded":1,"abstract":[{"text":"Using extensive direct numerical simulations, the dynamics of laminar-turbulent fronts in pipe flow is investigated for Reynolds numbers between and 5500. We here investigate the physical distinction between the fronts of weak and strong slugs both by analysing the turbulent kinetic energy budget and by comparing the downstream front motion to the advection speed of bulk turbulent structures. Our study shows that weak downstream fronts travel slower than turbulent structures in the bulk and correspond to decaying turbulence at the front. At the downstream front speed becomes faster than the advection speed, marking the onset of strong fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts by feeding on the downstream laminar flow. Our study also suggests that temporal fluctuations of production and dissipation at the downstream laminar-turbulent front drive the dynamical switches between the two types of front observed up to.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"BjHo"}],"project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000394376400044"]},"_id":"1087","language":[{"iso":"eng"}],"publication_status":"published","oa_version":"Submitted Version","publist_id":"6290","doi":"10.1017/jfm.2017.14","year":"2017","type":"journal_article","isi":1,"scopus_import":"1","author":[{"full_name":"Song, Baofang","last_name":"Song","first_name":"Baofang"},{"full_name":"Barkley, Dwight","first_name":"Dwight","last_name":"Barkley"},{"last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"}],"oa":1,"status":"public","title":"Speed and structure of turbulent fronts in pipe flow","publication":"Journal of Fluid Mechanics","intvolume":" 813","page":"1045 - 1059","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.04077"}],"quality_controlled":"1","publisher":"Cambridge University Press","acknowledged_ssus":[{"_id":"ScienComp"}],"month":"02","date_published":"2017-02-25T00:00:00Z","date_created":"2018-12-11T11:50:04Z","volume":813,"date_updated":"2023-09-20T11:47:22Z","citation":{"ieee":"B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent fronts in pipe flow,” Journal of Fluid Mechanics, vol. 813. Cambridge University Press, pp. 1045–1059, 2017.","apa":"Song, B., Barkley, D., Hof, B., & Avila, M. (2017). Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.14","short":"B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017) 1045–1059.","chicago":"Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.14.","mla":"Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics, vol. 813, Cambridge University Press, 2017, pp. 1045–59, doi:10.1017/jfm.2017.14.","ista":"Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059.","ama":"Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 2017;813:1045-1059. doi:10.1017/jfm.2017.14"},"day":"25"},{"intvolume":" 45","publication":"Annals of Statistics","publisher":"Institute of Mathematical Statistics","page":"1152 - 1184","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1510.01290"}],"quality_controlled":"1","issue":"3","author":[{"full_name":"Fallat, Shaun","first_name":"Shaun","last_name":"Fallat"},{"last_name":"Lauritzen","first_name":"Steffen","full_name":"Lauritzen, Steffen"},{"full_name":"Sadeghi, Kayvan","last_name":"Sadeghi","first_name":"Kayvan"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","first_name":"Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler"},{"first_name":"Nanny","last_name":"Wermuth","full_name":"Wermuth, Nanny"},{"full_name":"Zwiernik, Piotr","first_name":"Piotr","last_name":"Zwiernik"}],"oa":1,"status":"public","title":"Total positivity in Markov structures","date_updated":"2023-09-20T11:46:53Z","day":"01","citation":{"ieee":"S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, and P. Zwiernik, “Total positivity in Markov structures,” Annals of Statistics, vol. 45, no. 3. Institute of Mathematical Statistics, pp. 1152–1184, 2017.","apa":"Fallat, S., Lauritzen, S., Sadeghi, K., Uhler, C., Wermuth, N., & Zwiernik, P. (2017). Total positivity in Markov structures. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AOS1478","short":"S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, P. Zwiernik, Annals of Statistics 45 (2017) 1152–1184.","chicago":"Fallat, Shaun, Steffen Lauritzen, Kayvan Sadeghi, Caroline Uhler, Nanny Wermuth, and Piotr Zwiernik. “Total Positivity in Markov Structures.” Annals of Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AOS1478.","mla":"Fallat, Shaun, et al. “Total Positivity in Markov Structures.” Annals of Statistics, vol. 45, no. 3, Institute of Mathematical Statistics, 2017, pp. 1152–84, doi:10.1214/16-AOS1478.","ama":"Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. Total positivity in Markov structures. Annals of Statistics. 2017;45(3):1152-1184. doi:10.1214/16-AOS1478","ista":"Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. 2017. Total positivity in Markov structures. Annals of Statistics. 45(3), 1152–1184."},"month":"06","date_created":"2018-12-11T11:50:05Z","date_published":"2017-06-01T00:00:00Z","volume":45,"department":[{"_id":"CaUh"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000404395900008"]},"project":[{"grant_number":"Y 903-N35","call_identifier":"FWF","_id":"2530CA10-B435-11E9-9278-68D0E5697425","name":"Gaussian Graphical Models: Theory and Applications"}],"publication_status":"published","language":[{"iso":"eng"}],"_id":"1089","article_processing_charge":"No","publication_identifier":{"issn":["00905364"]},"abstract":[{"lang":"eng","text":"We discuss properties of distributions that are multivariate totally positive of order two (MTP2) related to conditional independence. In particular, we show that any independence model generated by an MTP2 distribution is a compositional semigraphoid which is upward-stable and singleton-transitive. In addition, we prove that any MTP2 distribution satisfying an appropriate support condition is faithful to its concentration graph. Finally, we analyze factorization properties of MTP2 distributions and discuss ways of constructing MTP2 distributions; in particular we give conditions on the log-linear parameters of a discrete distribution which ensure MTP2 and characterize conditional Gaussian distributions which satisfy MTP2."}],"scopus_import":"1","year":"2017","isi":1,"type":"journal_article","oa_version":"Submitted Version","publist_id":"6288","doi":"10.1214/16-AOS1478"},{"oa":1,"author":[{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"first_name":"Ulisse","last_name":"Ferrari","full_name":"Ferrari, Ulisse"},{"full_name":"Mace, Emilie","last_name":"Mace","first_name":"Emilie"},{"first_name":"Pierre","last_name":"Yger","full_name":"Yger, Pierre"},{"first_name":"Romain","last_name":"Caplette","full_name":"Caplette, Romain"},{"full_name":"Picaud, Serge","first_name":"Serge","last_name":"Picaud"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"}],"title":"Multiplexed computations in retinal ganglion cells of a single type","article_number":"1964","status":"public","quality_controlled":"1","publisher":"Nature Publishing Group","publication":"Nature Communications","intvolume":" 8","issue":"1","date_created":"2018-12-11T11:50:10Z","date_published":"2017-12-06T00:00:00Z","month":"12","has_accepted_license":"1","volume":8,"citation":{"ama":"Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y","ista":"Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O. 2017. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 8(1), 1964.","mla":"Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:10.1038/s41467-017-02159-y.","chicago":"Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-02159-y.","short":"S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017).","apa":"Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre, O. (2017). Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02159-y","ieee":"S. Deny et al., “Multiplexed computations in retinal ganglion cells of a single type,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017."},"day":"06","file":[{"file_name":"IST-2018-921-v1+1_s41467-017-02159-y.pdf","date_updated":"2018-12-12T10:16:06Z","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:16:06Z","creator":"system","file_id":"5191","relation":"main_file","file_size":2872887}],"date_updated":"2023-09-20T11:41:19Z","file_date_updated":"2018-12-12T10:16:06Z","publication_identifier":{"issn":["20411723"]},"article_processing_charge":"No","abstract":[{"lang":"eng","text":"In the early visual system, cells of the same type perform the same computation in different places of the visual field. How these cells code together a complex visual scene is unclear. A common assumption is that cells of a single-type extract a single-stimulus feature to form a feature map, but this has rarely been observed directly. Using large-scale recordings in the rat retina, we show that a homogeneous population of fast OFF ganglion cells simultaneously encodes two radically different features of a visual scene. Cells close to a moving object code quasilinearly for its position, while distant cells remain largely invariant to the object's position and, instead, respond nonlinearly to changes in the object's speed. We develop a quantitative model that accounts for this effect and identify a disinhibitory circuit that mediates it. Ganglion cells of a single type thus do not code for one, but two features simultaneously. This richer, flexible neural map might also be present in other sensory systems."}],"ec_funded":1,"project":[{"name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","call_identifier":"FP7","grant_number":"604102","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425"},{"name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","call_identifier":"FWF"}],"external_id":{"isi":["000417241200004"]},"department":[{"_id":"GaTk"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"_id":"1104","publication_status":"published","ddc":["571"],"oa_version":"Published Version","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"},"publist_id":"6266","doi":"10.1038/s41467-017-02159-y","pubrep_id":"921","type":"journal_article","year":"2017","isi":1,"scopus_import":"1"},{"volume":54,"month":"04","date_created":"2018-12-11T11:50:11Z","date_published":"2017-04-01T00:00:00Z","conference":{"end_date":"2017-04-22","start_date":"2017-04-20","location":"Fort Lauderdale, FL, United States","name":"AISTATS: Artificial Intelligence and Statistics"},"date_updated":"2023-10-17T10:01:12Z","citation":{"chicago":"Zimin, Alexander, and Christoph Lampert. “Learning Theory for Conditional Risk Minimization,” 54:213–22. ML Research Press, 2017.","ama":"Zimin A, Lampert C. Learning theory for conditional risk minimization. In: Vol 54. ML Research Press; 2017:213-222.","ista":"Zimin A, Lampert C. 2017. Learning theory for conditional risk minimization. AISTATS: Artificial Intelligence and Statistics, PMLR, vol. 54, 213–222.","mla":"Zimin, Alexander, and Christoph Lampert. Learning Theory for Conditional Risk Minimization. Vol. 54, ML Research Press, 2017, pp. 213–22.","apa":"Zimin, A., & Lampert, C. (2017). Learning theory for conditional risk minimization (Vol. 54, pp. 213–222). Presented at the AISTATS: Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States: ML Research Press.","short":"A. Zimin, C. Lampert, in:, ML Research Press, 2017, pp. 213–222.","ieee":"A. Zimin and C. Lampert, “Learning theory for conditional risk minimization,” presented at the AISTATS: Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 213–222."},"day":"01","status":"public","title":"Learning theory for conditional risk minimization","author":[{"id":"37099E9C-F248-11E8-B48F-1D18A9856A87","full_name":"Zimin, Alexander","last_name":"Zimin","first_name":"Alexander"},{"orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"intvolume":" 54","main_file_link":[{"open_access":"1","url":"http://proceedings.mlr.press/v54/zimin17a/zimin17a.pdf"}],"page":"213 - 222","quality_controlled":"1","publisher":"ML Research Press","publist_id":"6261","oa_version":"Submitted Version","year":"2017","type":"conference","isi":1,"ec_funded":1,"abstract":[{"lang":"eng","text":"In this work we study the learnability of stochastic processes with respect to the conditional risk, i.e. the existence of a learning algorithm that improves its next-step performance with the amount of observed data. We introduce a notion of pairwise discrepancy between conditional distributions at different times steps and show how certain properties of these discrepancies can be used to construct a successful learning algorithm. Our main results are two theorems that establish criteria for learnability for many classes of stochastic processes, including all special cases studied previously in the literature."}],"article_processing_charge":"No","alternative_title":["PMLR"],"_id":"1108","language":[{"iso":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"}],"project":[{"call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"external_id":{"isi":["000509368500024"]}},{"article_number":"203203","title":"Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free","status":"public","oa":1,"author":[{"full_name":"Shepperson, Benjamin","last_name":"Shepperson","first_name":"Benjamin"},{"last_name":"Søndergaard","first_name":"Anders","full_name":"Søndergaard, Anders"},{"first_name":"Lars","last_name":"Christiansen","full_name":"Christiansen, Lars"},{"full_name":"Kaczmarczyk, Jan","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarczyk","orcid":"0000-0002-1629-3675","first_name":"Jan"},{"first_name":"Robert","last_name":"Zillich","full_name":"Zillich, Robert"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail"},{"last_name":"Stapelfeldt","first_name":"Henrik","full_name":"Stapelfeldt, Henrik"}],"issue":"20","publisher":"American Physical Society","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1702.01977","open_access":"1"}],"intvolume":" 118","publication":"Physical Review Letters","volume":118,"date_published":"2017-05-19T00:00:00Z","date_created":"2018-12-11T11:50:12Z","month":"05","citation":{"chicago":"Shepperson, Benjamin, Anders Søndergaard, Lars Christiansen, Jan Kaczmarczyk, Robert Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Laser-Induced Rotation of Iodine Molecules in Helium Nanodroplets: Revivals and Breaking-Free.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.203203.","ista":"Shepperson B, Søndergaard A, Christiansen L, Kaczmarczyk J, Zillich R, Lemeshko M, Stapelfeldt H. 2017. Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. 118(20), 203203.","ama":"Shepperson B, Søndergaard A, Christiansen L, et al. Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. 2017;118(20). doi:10.1103/PhysRevLett.118.203203","mla":"Shepperson, Benjamin, et al. “Laser-Induced Rotation of Iodine Molecules in Helium Nanodroplets: Revivals and Breaking-Free.” Physical Review Letters, vol. 118, no. 20, 203203, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.203203.","short":"B. Shepperson, A. Søndergaard, L. Christiansen, J. Kaczmarczyk, R. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 118 (2017).","apa":"Shepperson, B., Søndergaard, A., Christiansen, L., Kaczmarczyk, J., Zillich, R., Lemeshko, M., & Stapelfeldt, H. (2017). Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.203203","ieee":"B. Shepperson et al., “Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free,” Physical Review Letters, vol. 118, no. 20. American Physical Society, 2017."},"day":"19","date_updated":"2023-09-20T11:36:17Z","abstract":[{"lang":"eng","text":"Rotation of molecules embedded in He nanodroplets is explored by a combination of fs laser-induced alignment experiments and angulon quasiparticle theory. We demonstrate that at low fluence of the fs alignment pulse, the molecule and its solvation shell can be set into coherent collective rotation lasting long enough to form revivals. With increasing fluence, however, the revivals disappear -- instead, rotational dynamics as rapid as for an isolated molecule is observed during the first few picoseconds. Classical calculations trace this phenomenon to transient decoupling of the molecule from its He shell. Our results open novel opportunities for studying non-equilibrium solute-solvent dynamics and quantum thermalization. "}],"article_processing_charge":"No","publication_status":"published","language":[{"iso":"eng"}],"_id":"1109","external_id":{"isi":["000401664000005"]},"project":[{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"MiLe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1103/PhysRevLett.118.203203","publist_id":"6260","oa_version":"Preprint","scopus_import":"1","isi":1,"type":"journal_article","year":"2017"},{"publisher":"Nature Publishing Group","quality_controlled":"1","intvolume":" 7","publication":"Scientific Reports","article_number":"41906","title":"Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity","status":"public","oa":1,"author":[{"last_name":"Kuhn","first_name":"Benjamin","full_name":"Kuhn, Benjamin"},{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"full_name":"Errafi, Sanae","last_name":"Errafi","first_name":"Sanae"},{"full_name":"Bucher, Rahel","last_name":"Bucher","first_name":"Rahel"},{"full_name":"Gupta, Shibu","first_name":"Shibu","last_name":"Gupta"},{"full_name":"Aryal, Bibek","last_name":"Aryal","first_name":"Bibek"},{"first_name":"Petre","last_name":"Dobrev","full_name":"Dobrev, Petre"},{"full_name":"Bigler, Laurent","last_name":"Bigler","first_name":"Laurent"},{"full_name":"Geisler, Markus","last_name":"Geisler","first_name":"Markus"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"full_name":"Ringli, Christoph","first_name":"Christoph","last_name":"Ringli"}],"file":[{"relation":"main_file","file_id":"5328","creator":"system","file_size":1654496,"date_created":"2018-12-12T10:18:09Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2018-12-12T10:18:09Z","file_name":"IST-2017-803-v1+1_srep41906.pdf"}],"citation":{"mla":"Kuhn, Benjamin, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” Scientific Reports, vol. 7, 41906, Nature Publishing Group, 2017, doi:10.1038/srep41906.","ista":"Kuhn B, Nodzyński T, Errafi S, Bucher R, Gupta S, Aryal B, Dobrev P, Bigler L, Geisler M, Zažímalová E, Friml J, Ringli C. 2017. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. 7, 41906.","ama":"Kuhn B, Nodzyński T, Errafi S, et al. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. 2017;7. doi:10.1038/srep41906","chicago":"Kuhn, Benjamin, Tomasz Nodzyński, Sanae Errafi, Rahel Bucher, Shibu Gupta, Bibek Aryal, Petre Dobrev, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41906.","ieee":"B. Kuhn et al., “Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity,” Scientific Reports, vol. 7. Nature Publishing Group, 2017.","short":"B. Kuhn, T. Nodzyński, S. Errafi, R. Bucher, S. Gupta, B. Aryal, P. Dobrev, L. Bigler, M. Geisler, E. Zažímalová, J. Friml, C. Ringli, Scientific Reports 7 (2017).","apa":"Kuhn, B., Nodzyński, T., Errafi, S., Bucher, R., Gupta, S., Aryal, B., … Ringli, C. (2017). Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep41906"},"day":"06","date_updated":"2025-05-07T11:12:29Z","has_accepted_license":"1","volume":7,"date_published":"2017-02-06T00:00:00Z","date_created":"2018-12-11T11:50:12Z","month":"02","ddc":["581"],"publication_status":"published","_id":"1110","language":[{"iso":"eng"}],"external_id":{"isi":["000393367600001"]},"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"abstract":[{"text":"The phytohormone auxin is a major determinant and regulatory component important for plant development. Auxin transport between cells is mediated by a complex system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization and activity is thought to be influenced by phosphatases and kinases. Flavonols have been shown to alter auxin transport activity and changes in flavonol accumulation in the Arabidopsis thaliana rol1-2 mutant cause defects in auxin transport and seedling development. A new mutation in ROOTS CURL IN NPA 1 (RCN1), encoding a regulatory subunit of the phosphatase PP2A, was found to suppress the growth defects of rol1-2 without changing the flavonol content. rol1-2 rcn1-3 double mutants show wild type-like auxin transport activity while levels of free auxin are not affected by rcn1-3. In the rol1-2 mutant, PIN2 shows a flavonol-induced basal-to-apical shift in polar localization which is reversed in the rol1-2 rcn1-3 to basal localization. In vivo analysis of PINOID action, a kinase known to influence PIN protein localization in a PP2A-antagonistic manner, revealed a negative impact of flavonols on PINOID activity. Together, these data suggest that flavonols affect auxin transport by modifying the antagonistic kinase/phosphatase equilibrium.","lang":"eng"}],"ec_funded":1,"publication_identifier":{"issn":["20452322"]},"file_date_updated":"2018-12-12T10:18:09Z","acknowledgement":"European Research Council (project ERC-2011-StG-20101109-PSDP), European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation (GA13-40637S) [JF].","article_processing_charge":"No","scopus_import":"1","year":"2017","type":"journal_article","isi":1,"pubrep_id":"803","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"},"publist_id":"6258","doi":"10.1038/srep41906","oa_version":"Published Version"},{"pmid":1,"oa_version":"Published Version","publist_id":"6256","doi":"10.1534/genetics.116.189340","scopus_import":"1","isi":1,"year":"2017","type":"journal_article","article_processing_charge":"No","publication_identifier":{"issn":["00166731"]},"ec_funded":1,"abstract":[{"lang":"eng","text":"Adaptation depends critically on the effects of new mutations and their dependency on the genetic background in which they occur. These two factors can be summarized by the fitness landscape. However, it would require testing all mutations in all backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible. Instead of postulating a particular fitness landscape, we address this problem by considering general classes of landscapes and calculating an upper limit for the time it takes for a population to reach a fitness peak, circumventing the need to have full knowledge about the fitness landscape. We analyze populations in the weak-mutation regime and characterize the conditions that enable them to quickly reach the fitness peak as a function of the number of sites under selection. We show that for additive landscapes there is a critical selection strength enabling populations to reach high-fitness genotypes, regardless of the distribution of effects. This threshold scales with the number of sites under selection, effectively setting a limit to adaptation, and results from the inevitable increase in deleterious mutational pressure as the population adapts in a space of discrete genotypes. Furthermore, we show that for the class of all unimodal landscapes this condition is sufficient but not necessary for rapid adaptation, as in some highly epistatic landscapes the critical strength does not depend on the number of sites under selection; effectively removing this barrier to adaptation."}],"department":[{"_id":"NiBa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000394144900025"],"pmid":["27881471"]},"project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"publication_status":"published","language":[{"iso":"eng"}],"_id":"1111","month":"02","date_created":"2018-12-11T11:50:12Z","date_published":"2017-02-01T00:00:00Z","volume":205,"article_type":"original","date_updated":"2023-09-20T11:35:03Z","citation":{"short":"J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825.","apa":"Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection limits to adaptive walks on correlated landscapes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.189340","ieee":"J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics Society of America, pp. 803–825, 2017.","ama":"Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340","ista":"Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive walks on correlated landscapes. Genetics. 205(2), 803–825.","mla":"Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25, doi:10.1534/genetics.116.189340.","chicago":"Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.189340."},"day":"01","author":[{"full_name":"Heredia, Jorge","last_name":"Heredia","first_name":"Jorge"},{"full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","last_name":"Trubenova","first_name":"Barbora"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"}],"oa":1,"status":"public","title":"Selection limits to adaptive walks on correlated landscapes","intvolume":" 205","publication":"Genetics","publisher":"Genetics Society of America","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1534/genetics.116.189340","open_access":"1"}],"page":"803 - 825","issue":"2"},{"oa_version":"None","date_created":"2018-12-11T11:50:12Z","date_published":"2017-01-12T00:00:00Z","month":"01","doi":"10.1145/3040718.3040729","publist_id":"6255","citation":{"mla":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.","ama":"Paixao T, Pérez Heredia J. An application of stochastic differential equations to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729","ista":"Paixao T, Pérez Heredia J. 2017. An application of stochastic differential equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms, 3–11.","chicago":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729.","ieee":"T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11.","short":"T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11.","apa":"Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential equations to evolutionary algorithms. In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms (pp. 3–11). Copenhagen, Denmark: ACM. https://doi.org/10.1145/3040718.3040729"},"day":"12","date_updated":"2021-01-12T06:48:22Z","scopus_import":1,"type":"conference","year":"2017","conference":{"end_date":"2017-01-15","start_date":"2017-01-12","location":"Copenhagen, Denmark","name":"FOGA: Foundations of Genetic Algorithms"},"publication_identifier":{"isbn":["978-145034651-1"]},"author":[{"first_name":"Tiago","last_name":"Paixao","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"first_name":"Jorge","last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge"}],"abstract":[{"text":"There has been renewed interest in modelling the behaviour of evolutionary algorithms by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics. On the other hand, unlike ordinary differential equations (ODEs), they do not discard information about the stochasticity of the process. We show that these are especially suitable for the analysis of fixed budget scenarios and present analogs of the additive and multiplicative drift theorems for SDEs. We exemplify the use of these methods for two model algorithms ((1+1) EA and RLS) on two canonical problems(OneMax and LeadingOnes).","lang":"eng"}],"title":"An application of stochastic differential equations to evolutionary algorithms","status":"public","publisher":"ACM","page":"3 - 11","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"publication":"Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms","publication_status":"published","_id":"1112","language":[{"iso":"eng"}]},{"scopus_import":1,"year":"2017","type":"journal_article","arxiv":1,"oa_version":"Published Version","publist_id":"6254","doi":"10.7155/jgaa.00408","department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1608.08662"]},"project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"ddc":["510"],"publication_status":"published","_id":"1113","language":[{"iso":"eng"}],"article_processing_charge":"No","file_date_updated":"2019-10-24T10:54:37Z","ec_funded":1,"abstract":[{"lang":"eng","text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C 1 , . . . , C k with common center c , and edges are drawn radially : every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Toth."}],"date_updated":"2023-02-23T10:05:57Z","file":[{"relation":"main_file","file_id":"6967","creator":"dernst","file_size":573623,"date_created":"2019-10-24T10:54:37Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2019-10-24T10:54:37Z","file_name":"2017_JournalGraphAlgorithms_Fulek.pdf","success":1}],"citation":{"ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” Journal of Graph Algorithms and Applications, vol. 21, no. 1. Brown University, pp. 135–154, 2017.","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2017). Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00408","short":"R. Fulek, M. Pelsmajer, M. Schaefer, Journal of Graph Algorithms and Applications 21 (2017) 135–154.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications. Brown University, 2017. https://doi.org/10.7155/jgaa.00408.","mla":"Fulek, Radoslav, et al. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications, vol. 21, no. 1, Brown University, 2017, pp. 135–54, doi:10.7155/jgaa.00408.","ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 2017;21(1):135-154. doi:10.7155/jgaa.00408","ista":"Fulek R, Pelsmajer M, Schaefer M. 2017. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 21(1), 135–154."},"day":"01","related_material":{"record":[{"status":"public","id":"1164","relation":"earlier_version"},{"status":"public","id":"1595","relation":"earlier_version"}]},"month":"01","date_created":"2018-12-11T11:50:13Z","date_published":"2017-01-01T00:00:00Z","volume":21,"article_type":"original","has_accepted_license":"1","intvolume":" 21","publication":"Journal of Graph Algorithms and Applications","publisher":"Brown University","quality_controlled":"1","page":"135 - 154","issue":"1","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774","first_name":"Radoslav"},{"first_name":"Michael","last_name":"Pelsmajer","full_name":"Pelsmajer, Michael"},{"full_name":"Schaefer, Marcus","first_name":"Marcus","last_name":"Schaefer"}],"oa":1,"status":"public","title":"Hanani-Tutte for radial planarity"},{"abstract":[{"lang":"eng","text":"Nonequilibrium phase transitions exist in damped-driven open quantum systems when the continuous tuning of an external parameter leads to a transition between two robust steady states. In second-order transitions this change is abrupt at a critical point, whereas in first-order transitions the two phases can coexist in a critical hysteresis domain. Here, we report the observation of a first-order dissipative quantum phase transition in a driven circuit quantum electrodynamics system. It takes place when the photon blockade of the driven cavity-atom system is broken by increasing the drive power. The observed experimental signature is a bimodal phase space distribution with varying weights controlled by the drive strength. Our measurements show an improved stabilization of the classical attractors up to the millisecond range when the size of the quantum system is increased from one to three artificial atoms. The formation of such robust pointer states could be used for new quantum measurement schemes or to investigate multiphoton phases of finite-size, nonlinear, open quantum systems."}],"article_processing_charge":"Yes","publication_identifier":{"issn":["21603308"]},"file_date_updated":"2018-12-12T10:12:52Z","publication_status":"published","ddc":["539"],"_id":"1114","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000397450500001"]},"doi":"10.1103/PhysRevX.7.011012","publist_id":"6252","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_version":"Published Version","scopus_import":"1","year":"2017","isi":1,"type":"journal_article","pubrep_id":"753","status":"public","article_number":"011012","title":"Observation of the photon blockade breakdown phase transition","author":[{"full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink"},{"full_name":"Dombi, András","first_name":"András","last_name":"Dombi"},{"first_name":"András","last_name":"Vukics","full_name":"Vukics, András"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"},{"first_name":"Peter","last_name":"Domokos","full_name":"Domokos, Peter"}],"oa":1,"issue":"1","intvolume":" 7","publication":"Physical Review X","publisher":"American Physical Society","quality_controlled":"1","volume":7,"has_accepted_license":"1","month":"01","date_created":"2018-12-11T11:50:13Z","date_published":"2017-01-31T00:00:00Z","date_updated":"2023-09-20T11:33:07Z","file":[{"date_created":"2018-12-12T10:12:52Z","creator":"system","file_id":"4972","relation":"main_file","file_size":1172926,"access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-753-v1+1_PhysRevX.7.011012.pdf","date_updated":"2018-12-12T10:12:52Z"}],"citation":{"chicago":"Fink, Johannes M, András Dombi, András Vukics, Andreas Wallraff, and Peter Domokos. “Observation of the Photon Blockade Breakdown Phase Transition.” Physical Review X. American Physical Society, 2017. https://doi.org/10.1103/PhysRevX.7.011012.","ama":"Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. Observation of the photon blockade breakdown phase transition. Physical Review X. 2017;7(1). doi:10.1103/PhysRevX.7.011012","ista":"Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. 2017. Observation of the photon blockade breakdown phase transition. Physical Review X. 7(1), 011012.","mla":"Fink, Johannes M., et al. “Observation of the Photon Blockade Breakdown Phase Transition.” Physical Review X, vol. 7, no. 1, 011012, American Physical Society, 2017, doi:10.1103/PhysRevX.7.011012.","short":"J.M. Fink, A. Dombi, A. Vukics, A. Wallraff, P. Domokos, Physical Review X 7 (2017).","apa":"Fink, J. M., Dombi, A., Vukics, A., Wallraff, A., & Domokos, P. (2017). Observation of the photon blockade breakdown phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.7.011012","ieee":"J. M. Fink, A. Dombi, A. Vukics, A. Wallraff, and P. Domokos, “Observation of the photon blockade breakdown phase transition,” Physical Review X, vol. 7, no. 1. American Physical Society, 2017."},"day":"31"},{"oa_version":"Submitted Version","publist_id":"6246","doi":"10.1007/978-3-662-54580-5_10","pubrep_id":"758","scopus_import":"1","isi":1,"year":"2017","type":"conference","alternative_title":["LNCS"],"article_processing_charge":"No","publication_identifier":{"issn":["03029743"]},"file_date_updated":"2018-12-12T10:08:37Z","abstract":[{"lang":"eng","text":"Time-triggered switched networks are a deterministic communication infrastructure used by real-time distributed embedded systems. Due to the criticality of the applications running over them, developers need to ensure that end-to-end communication is dependable and predictable. Traditional approaches assume static networks that are not flexible to changes caused by reconfigurations or, more importantly, faults, which are dealt with in the application using redundancy. We adopt the concept of handling faults in the switches from non-real-time networks while maintaining the required predictability. \r\n\r\nWe study a class of forwarding schemes that can handle various types of failures. We consider probabilistic failures. We study a class of forwarding schemes that can handle various types of failures. We consider probabilistic failures. For a given network with a forwarding scheme and a constant ℓ, we compute the {\\em score} of the scheme, namely the probability (induced by faults) that at least ℓ messages arrive on time. We reduce the scoring problem to a reachability problem on a Markov chain with a "product-like" structure. Its special structure allows us to reason about it symbolically, and reduce the scoring problem to #SAT. Our solution is generic and can be adapted to different networks and other contexts. Also, we show the computational complexity of the scoring problem is #P-complete, and we study methods to estimate the score. We evaluate the effectiveness of our techniques with an implementation. "}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"ToHe"}],"external_id":{"isi":["000440733400010"]},"project":[{"grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211"}],"publication_status":"published","ddc":["000"],"language":[{"iso":"eng"}],"_id":"1116","month":"03","date_published":"2017-03-31T00:00:00Z","date_created":"2018-12-11T11:50:14Z","volume":10206,"has_accepted_license":"1","date_updated":"2023-09-20T11:32:43Z","file":[{"date_updated":"2018-12-12T10:08:37Z","file_name":"IST-2017-758-v1+1_tacas-cr.pdf","content_type":"application/pdf","access_level":"open_access","file_size":321800,"creator":"system","relation":"main_file","file_id":"4698","date_created":"2018-12-12T10:08:37Z"}],"citation":{"mla":"Avni, Guy, et al. Computing Scores of Forwarding Schemes in Switched Networks with Probabilistic Faults. Vol. 10206, Springer, 2017, pp. 169–87, doi:10.1007/978-3-662-54580-5_10.","ista":"Avni G, Goel S, Henzinger TA, Rodríguez Navas G. 2017. Computing scores of forwarding schemes in switched networks with probabilistic faults. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10206, 169–187.","ama":"Avni G, Goel S, Henzinger TA, Rodríguez Navas G. Computing scores of forwarding schemes in switched networks with probabilistic faults. In: Vol 10206. Springer; 2017:169-187. doi:10.1007/978-3-662-54580-5_10","chicago":"Avni, Guy, Shubham Goel, Thomas A Henzinger, and Guillermo Rodríguez Navas. “Computing Scores of Forwarding Schemes in Switched Networks with Probabilistic Faults,” 10206:169–87. Springer, 2017. https://doi.org/10.1007/978-3-662-54580-5_10.","ieee":"G. Avni, S. Goel, T. A. Henzinger, and G. Rodríguez Navas, “Computing scores of forwarding schemes in switched networks with probabilistic faults,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10206, pp. 169–187.","short":"G. Avni, S. Goel, T.A. Henzinger, G. Rodríguez Navas, in:, Springer, 2017, pp. 169–187.","apa":"Avni, G., Goel, S., Henzinger, T. A., & Rodríguez Navas, G. (2017). Computing scores of forwarding schemes in switched networks with probabilistic faults (Vol. 10206, pp. 169–187). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54580-5_10"},"day":"31","conference":{"end_date":"2017-04-29","location":"Uppsala, Sweden","start_date":"2017-04-22","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"author":[{"first_name":"Guy","last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goel, Shubham","first_name":"Shubham","last_name":"Goel"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"last_name":"Rodríguez Navas","first_name":"Guillermo","full_name":"Rodríguez Navas, Guillermo"}],"oa":1,"status":"public","title":"Computing scores of forwarding schemes in switched networks with probabilistic faults","intvolume":" 10206","publisher":"Springer","quality_controlled":"1","page":"169 - 187"},{"oa_version":"Published Version","publist_id":"6245","doi":"10.1016/j.celrep.2016.12.067","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"},"pubrep_id":"751","isi":1,"year":"2017","type":"journal_article","scopus_import":"1","article_processing_charge":"No","file_date_updated":"2018-12-12T10:16:09Z","publication_identifier":{"issn":["22111247"]},"ec_funded":1,"abstract":[{"lang":"eng","text":"GABAergic synapses in brain circuits generate inhibitory output signals with submillisecond latency and temporal precision. Whether the molecular identity of the release sensor contributes to these signaling properties remains unclear. Here, we examined the Ca^2+ sensor of exocytosis at GABAergic basket cell (BC) to Purkinje cell (PC) synapses in cerebellum. Immunolabeling suggested that BC terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin 1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced action potential-evoked release to ∼10%, identifying Syt2 as the major Ca^2+ sensor at BC-PC synapses. Differential adenovirus-mediated rescue revealed that Syt2 triggered release with shorter latency and higher temporal precision and mediated faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely reduced and delayed disynaptic inhibition following parallel fiber stimulation. Thus, the selective use of Syt2 as release sensor at BC-PC synapses ensures fast and efficient feedforward inhibition in cerebellar microcircuits. #bioimagingfacility-author"}],"department":[{"_id":"PeJo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548"}],"external_id":{"isi":["000396470600013"]},"language":[{"iso":"eng"}],"_id":"1117","publication_status":"published","ddc":["571"],"month":"01","date_created":"2018-12-11T11:50:14Z","date_published":"2017-01-17T00:00:00Z","volume":18,"has_accepted_license":"1","date_updated":"2023-09-20T11:32:15Z","citation":{"short":"C. Chen, itaru Arai, R. Satterield, S. Young, P.M. Jonas, Cell Reports 18 (2017) 723–736.","apa":"Chen, C., Arai, itaru, Satterield, R., Young, S., & Jonas, P. M. (2017). Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.12.067","ieee":"C. Chen, itaru Arai, R. Satterield, S. Young, and P. M. Jonas, “Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse,” Cell Reports, vol. 18, no. 3. Cell Press, pp. 723–736, 2017.","ama":"Chen C, Arai itaru, Satterield R, Young S, Jonas PM. Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. 2017;18(3):723-736. doi:10.1016/j.celrep.2016.12.067","ista":"Chen C, Arai itaru, Satterield R, Young S, Jonas PM. 2017. Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. 18(3), 723–736.","mla":"Chen, Chong, et al. “Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory Synapse.” Cell Reports, vol. 18, no. 3, Cell Press, 2017, pp. 723–36, doi:10.1016/j.celrep.2016.12.067.","chicago":"Chen, Chong, itaru Arai, Rachel Satterield, Samuel Young, and Peter M Jonas. “Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory Synapse.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2016.12.067."},"day":"17","file":[{"file_size":4427591,"file_id":"5195","relation":"main_file","creator":"system","date_created":"2018-12-12T10:16:09Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2018-12-12T10:16:09Z","file_name":"IST-2017-751-v1+1_1-s2.0-S2211124716317740-main.pdf"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"324"}]},"author":[{"full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chong"},{"last_name":"Arai","first_name":"Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","full_name":"Arai, Itaru"},{"full_name":"Satterield, Rachel","first_name":"Rachel","last_name":"Satterield"},{"last_name":"Young","first_name":"Samuel","full_name":"Young, Samuel"},{"first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"}],"oa":1,"status":"public","title":"Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse","publication":"Cell Reports","intvolume":" 18","page":"723 - 736","quality_controlled":"1","publisher":"Cell Press","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"issue":"3"},{"type":"journal_article","year":"2017","isi":1,"scopus_import":"1","pubrep_id":"752","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"},"doi":"10.1016/j.neuron.2016.12.018","publist_id":"6244","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"1118","ddc":["571"],"publication_status":"published","project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24","call_identifier":"FWF"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548"}],"external_id":{"isi":["000396428200010"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"PeJo"},{"_id":"JoCs"}],"abstract":[{"lang":"eng","text":"Sharp wave-ripple (SWR) oscillations play a key role in memory consolidation during non-rapid eye movement sleep, immobility, and consummatory behavior. However, whether temporally modulated synaptic excitation or inhibition underlies the ripples is controversial. To address this question, we performed simultaneous recordings of excitatory and inhibitory postsynaptic currents (EPSCs and IPSCs) and local field potentials (LFPs) in the CA1 region of awake mice in vivo. During SWRs, inhibition dominated over excitation, with a peak conductance ratio of 4.1 ± 0.5. Furthermore, the amplitude of SWR-associated IPSCs was positively correlated with SWR magnitude, whereas that of EPSCs was not. Finally, phase analysis indicated that IPSCs were phase-locked to individual ripple cycles, whereas EPSCs were uniformly distributed in phase space. Optogenetic inhibition indicated that PV+ interneurons provided a major contribution to SWR-associated IPSCs. Thus, phasic inhibition, but not excitation, shapes SWR oscillations in the hippocampal CA1 region in vivo."}],"ec_funded":1,"file_date_updated":"2018-12-12T10:08:56Z","article_processing_charge":"No","day":"18","citation":{"ieee":"J. Gan, S.-M. Weng, A. Pernia-Andrade, J. L. Csicsvari, and P. M. Jonas, “Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo,” Neuron, vol. 93, no. 2. Elsevier, pp. 308–314, 2017.","apa":"Gan, J., Weng, S.-M., Pernia-Andrade, A., Csicsvari, J. L., & Jonas, P. M. (2017). Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2016.12.018","short":"J. Gan, S.-M. Weng, A. Pernia-Andrade, J.L. Csicsvari, P.M. Jonas, Neuron 93 (2017) 308–314.","mla":"Gan, Jian, et al. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal Ripple Oscillations in Awake Mice in Vivo.” Neuron, vol. 93, no. 2, Elsevier, 2017, pp. 308–14, doi:10.1016/j.neuron.2016.12.018.","ama":"Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. Neuron. 2017;93(2):308-314. doi:10.1016/j.neuron.2016.12.018","ista":"Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. 2017. Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. Neuron. 93(2), 308–314.","chicago":"Gan, Jian, Shih-Ming Weng, Alejandro Pernia-Andrade, Jozsef L Csicsvari, and Peter M Jonas. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal Ripple Oscillations in Awake Mice in Vivo.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2016.12.018."},"file":[{"creator":"system","file_id":"4719","relation":"main_file","file_size":2738950,"date_created":"2018-12-12T10:08:56Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2018-12-12T10:08:56Z","file_name":"IST-2017-752-v1+1_1-s2.0-S0896627316309606-main.pdf"}],"date_updated":"2023-09-20T11:31:48Z","has_accepted_license":"1","volume":93,"date_published":"2017-01-18T00:00:00Z","date_created":"2018-12-11T11:50:15Z","month":"01","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}],"issue":"2","quality_controlled":"1","page":"308 - 314","publisher":"Elsevier","publication":"Neuron","intvolume":" 93","title":"Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo","status":"public","oa":1,"author":[{"full_name":"Gan, Jian","id":"3614E438-F248-11E8-B48F-1D18A9856A87","first_name":"Jian","last_name":"Gan"},{"first_name":"Shih-Ming","last_name":"Weng","full_name":"Weng, Shih-Ming","id":"2F9C5AC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pernia-Andrade, Alejandro","id":"36963E98-F248-11E8-B48F-1D18A9856A87","first_name":"Alejandro","last_name":"Pernia-Andrade"},{"first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M"}]},{"day":"27","citation":{"short":"M. Lemeshko, Physical Review Letters 118 (2017).","apa":"Lemeshko, M. (2017). Quasiparticle approach to molecules interacting with quantum solvents. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.095301","ieee":"M. Lemeshko, “Quasiparticle approach to molecules interacting with quantum solvents,” Physical Review Letters, vol. 118, no. 9. American Physical Society, 2017.","ama":"Lemeshko M. Quasiparticle approach to molecules interacting with quantum solvents. Physical Review Letters. 2017;118(9). doi:10.1103/PhysRevLett.118.095301","ista":"Lemeshko M. 2017. Quasiparticle approach to molecules interacting with quantum solvents. Physical Review Letters. 118(9), 095301.","mla":"Lemeshko, Mikhail. “Quasiparticle Approach to Molecules Interacting with Quantum Solvents.” Physical Review Letters, vol. 118, no. 9, 095301, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.095301.","chicago":"Lemeshko, Mikhail. “Quasiparticle Approach to Molecules Interacting with Quantum Solvents.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.095301."},"date_updated":"2023-09-20T11:31:22Z","date_published":"2017-02-27T00:00:00Z","date_created":"2018-12-11T11:50:15Z","month":"02","volume":118,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.01604"}],"publisher":"American Physical Society","publication":"Physical Review Letters","intvolume":" 118","issue":"9","oa":1,"author":[{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"title":"Quasiparticle approach to molecules interacting with quantum solvents","article_number":"095301","status":"public","isi":1,"type":"journal_article","year":"2017","oa_version":"Submitted Version","doi":"10.1103/PhysRevLett.118.095301","publist_id":"6243","project":[{"grant_number":"11-NSF-1070","_id":"25636330-B435-11E9-9278-68D0E5697425","name":"ROOTS Genome-wide Analysis of Root Traits"}],"external_id":{"isi":["000404769200006"]},"department":[{"_id":"MiLe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"_id":"1119","publication_status":"published","publication_identifier":{"issn":["00319007"]},"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Understanding the behavior of molecules interacting with superfluid helium represents a formidable challenge and, in general, requires approaches relying on large-scale numerical simulations. Here we demonstrate that experimental data collected over the last 20 years provide evidence that molecules immersed in superfluid helium form recently-predicted angulon quasiparticles [Phys. Rev. Lett. 114, 203001 (2015)]. Most importantly, casting the many-body problem in terms of angulons amounts to a drastic simplification and yields effective molecular moments of inertia as straightforward analytic solutions of a simple microscopic Hamiltonian. The outcome of the angulon theory is in good agreement with experiment for a broad range of molecular impurities, from heavy to medium-mass to light species. These results pave the way to understanding molecular rotation in liquid and crystalline phases in terms of the angulon quasiparticle."}]}]