[{"author":[{"full_name":"Bevers, Roel P. J.","last_name":"Bevers","first_name":"Roel P. J."},{"first_name":"Maria","last_name":"Litovchenko","full_name":"Litovchenko, Maria"},{"full_name":"Kapopoulou, Adamandia","last_name":"Kapopoulou","first_name":"Adamandia"},{"last_name":"Braman","first_name":"Virginie S.","full_name":"Braman, Virginie S."},{"first_name":"Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"full_name":"Auwerx, Johan","last_name":"Auwerx","first_name":"Johan"},{"last_name":"Hollis","first_name":"Brian","full_name":"Hollis, Brian"},{"first_name":"Bart","last_name":"Deplancke","full_name":"Deplancke, Bart"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s42255-020-0202-0"}]},"date_updated":"2021-01-12T08:15:01Z","date_created":"2020-04-30T10:40:56Z","oa_version":"None","volume":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7711","year":"2019","status":"public","title":"Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel","publication_status":"published","publisher":"Springer Nature","intvolume":" 1","abstract":[{"lang":"eng","text":"The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies."}],"issue":"12","extern":"1","type":"journal_article","date_published":"2019-12-09T00:00:00Z","doi":"10.1038/s42255-019-0147-3","language":[{"iso":"eng"}],"publication":"Nature Metabolism","citation":{"short":"R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, Nature Metabolism 1 (2019) 1226–1242.","mla":"Bevers, Roel P. J., et al. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism, vol. 1, no. 12, Springer Nature, 2019, pp. 1226–42, doi:10.1038/s42255-019-0147-3.","chicago":"Bevers, Roel P. J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism. Springer Nature, 2019. https://doi.org/10.1038/s42255-019-0147-3.","ama":"Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 2019;1(12):1226-1242. doi:10.1038/s42255-019-0147-3","apa":"Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2019). Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-019-0147-3","ieee":"R. P. J. Bevers et al., “Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel,” Nature Metabolism, vol. 1, no. 12. Springer Nature, pp. 1226–1242, 2019.","ista":"Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2019. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 1(12), 1226–1242."},"quality_controlled":"1","article_type":"original","page":"1226-1242","month":"12","day":"09","article_processing_charge":"No","publication_identifier":{"issn":["2522-5812"]}},{"day":"14","month":"06","article_processing_charge":"No","page":"20","publication":"bioRxiv","citation":{"chicago":"Sulc, Jonathan, Ninon Mounier, Felix Günther, Thomas Winkler, Andrew R. Wood, Timothy M. Frayling, Iris M. Heid, Matthew Richard Robinson, and Zoltán Kutalik. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv. Cold Spring Harbor Laboratory, 2019.","short":"J. Sulc, N. Mounier, F. Günther, T. Winkler, A.R. Wood, T.M. Frayling, I.M. Heid, M.R. Robinson, Z. Kutalik, BioRxiv (2019).","mla":"Sulc, Jonathan, et al. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv, Cold Spring Harbor Laboratory, 2019.","ieee":"J. Sulc et al., “Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank,” bioRxiv. Cold Spring Harbor Laboratory, 2019.","apa":"Sulc, J., Mounier, N., Günther, F., Winkler, T., Wood, A. R., Frayling, T. M., … Kutalik, Z. (2019). Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. Cold Spring Harbor Laboratory.","ista":"Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson MR, Kutalik Z. 2019. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv, .","ama":"Sulc J, Mounier N, Günther F, et al. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. 2019."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/632380 "}],"language":[{"iso":"eng"}],"date_published":"2019-06-14T00:00:00Z","type":"preprint","extern":"1","abstract":[{"lang":"eng","text":"As genome-wide association studies (GWAS) increased in size, numerous gene-environment interactions (GxE) have been discovered, many of which however explore only one environment at a time and may suffer from statistical artefacts leading to biased interaction estimates. Here we propose a maximum likelihood method to estimate the contribution of GxE to complex traits taking into account all interacting environmental variables at the same time, without the need to measure any. This is possible because GxE induces fluctuations in the conditional trait variance, the extent of which depends on the strength of GxE. The approach can be applied to continuous outcomes and for single SNPs or genetic risk scores (GRS). Extensive simulations demonstrated that our method yields unbiased interaction estimates and excellent confidence interval coverage. We also offer a strategy to distinguish specific GxE from general heteroscedasticity (scale effects). Applying our method to 32 complex traits in the UK Biobank reveals that for body mass index (BMI) the GRSxE explains an additional 1.9% variance on top of the 5.2% GRS contribution. However, this interaction is not specific to the GRS and holds for any variable similarly correlated with BMI. On the contrary, the GRSxE interaction effect for leg impedance Embedded Image is significantly (P < 10−56) larger than it would be expected for a similarly correlated variable Embedded Image. We showed that our method could robustly detect the global contribution of GxE to complex traits, which turned out to be substantial for certain obesity measures."}],"publication_status":"published","title":"Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank","status":"public","publisher":"Cold Spring Harbor Laboratory","year":"2019","_id":"7782","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:15:30Z","date_created":"2020-04-30T13:04:26Z","oa_version":"Preprint","author":[{"first_name":"Jonathan","last_name":"Sulc","full_name":"Sulc, Jonathan"},{"first_name":"Ninon","last_name":"Mounier","full_name":"Mounier, Ninon"},{"last_name":"Günther","first_name":"Felix","full_name":"Günther, Felix"},{"first_name":"Thomas","last_name":"Winkler","full_name":"Winkler, Thomas"},{"full_name":"Wood, Andrew R.","first_name":"Andrew R.","last_name":"Wood"},{"last_name":"Frayling","first_name":"Timothy M.","full_name":"Frayling, Timothy M."},{"full_name":"Heid, Iris M.","last_name":"Heid","first_name":"Iris M."},{"last_name":"Robinson","first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"},{"first_name":"Zoltán","last_name":"Kutalik","full_name":"Kutalik, Zoltán"}]},{"month":"07","publication_identifier":{"issn":["1553-7358"]},"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31295253"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1007049","article_number":"e1007049","extern":"1","file_date_updated":"2020-07-14T12:48:08Z","publication_status":"published","publisher":"Public Library of Science","year":"2019","pmid":1,"date_created":"2020-06-25T12:50:39Z","date_updated":"2021-01-12T08:16:31Z","volume":15,"author":[{"first_name":"Christopher B.","last_name":"Currin","full_name":"Currin, Christopher B."},{"last_name":"Khoza","first_name":"Phumlani N.","full_name":"Khoza, Phumlani N."},{"full_name":"Antrobus, Alexander D.","first_name":"Alexander D.","last_name":"Antrobus"},{"full_name":"Latham, Peter E.","last_name":"Latham","first_name":"Peter E."},{"full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P"},{"last_name":"Raimondo","first_name":"Joseph V.","full_name":"Raimondo, Joseph V."}],"day":"11","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"PLOS Computational Biology","citation":{"chicago":"Currin, Christopher B., Phumlani N. Khoza, Alexander D. Antrobus, Peter E. Latham, Tim P Vogels, and Joseph V. Raimondo. “Think: Theory for Africa.” PLOS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007049.","short":"C.B. Currin, P.N. Khoza, A.D. Antrobus, P.E. Latham, T.P. Vogels, J.V. Raimondo, PLOS Computational Biology 15 (2019).","mla":"Currin, Christopher B., et al. “Think: Theory for Africa.” PLOS Computational Biology, vol. 15, no. 7, e1007049, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007049.","apa":"Currin, C. B., Khoza, P. N., Antrobus, A. D., Latham, P. E., Vogels, T. P., & Raimondo, J. V. (2019). Think: Theory for Africa. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007049","ieee":"C. B. Currin, P. N. Khoza, A. D. Antrobus, P. E. Latham, T. P. Vogels, and J. V. Raimondo, “Think: Theory for Africa,” PLOS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.","ista":"Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. 2019. Think: Theory for Africa. PLOS Computational Biology. 15(7), e1007049.","ama":"Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. Think: Theory for Africa. PLOS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007049"},"date_published":"2019-07-11T00:00:00Z","type":"journal_article","issue":"7","ddc":["570"],"title":"Think: Theory for Africa","status":"public","intvolume":" 15","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"8013","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_PlosCompBio_Currin.pdf","creator":"cziletti","content_type":"application/pdf","file_size":773969,"file_id":"8079","relation":"main_file","checksum":"723bdfb6ee5c747cbbb32baf01d17fad","date_created":"2020-07-02T12:22:57Z","date_updated":"2020-07-14T12:48:08Z"}]},{"file_date_updated":"2020-07-14T12:48:08Z","extern":"1","author":[{"full_name":"Manohar, Sanjay G.","last_name":"Manohar","first_name":"Sanjay G."},{"last_name":"Zokaei","first_name":"Nahid","full_name":"Zokaei, Nahid"},{"full_name":"Fallon, Sean J.","last_name":"Fallon","first_name":"Sean J."},{"full_name":"Vogels, Tim P","last_name":"Vogels","first_name":"Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425"},{"last_name":"Husain","first_name":"Masud","full_name":"Husain, Masud"}],"volume":101,"date_updated":"2021-01-12T08:16:31Z","date_created":"2020-06-25T12:52:13Z","pmid":1,"year":"2019","publisher":"Elsevier ","publication_status":"published","publication_identifier":{"issn":["0149-7634"]},"month":"06","doi":"10.1016/j.neubiorev.2019.03.017","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["30922977"]},"main_file_link":[{"url":"https://doi.org/10.1101/233007 ","open_access":"1"}],"oa":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"Working memory, the ability to keep recently accessed information available for immediate manipulation, has been proposed to rely on two mechanisms that appear difficult to reconcile: self-sustained neural firing, or the opposite—activity-silent synaptic traces. Here we review and contrast models of these two mechanisms, and then show that both phenomena can co-exist within a unified system in which neurons hold information in both activity and synapses. Rapid plasticity in flexibly-coding neurons allows features to be bound together into objects, with an important emergent property being the focus of attention. One memory item is held by persistent activity in an attended or “focused” state, and is thus remembered better than other items. Other, previously attended items can remain in memory but in the background, encoded in activity-silent synaptic traces. This dual functional architecture provides a unified common mechanism accounting for a diversity of perplexing attention and memory effects that have been hitherto difficult to explain in a single theoretical framework."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"8080","date_updated":"2020-07-14T12:48:08Z","date_created":"2020-07-02T13:17:52Z","checksum":"7b972e3d6f7bb3122c8c5648f44e60ca","file_name":"2019_NeurosBiobehavRev_Manohar.pdf","access_level":"open_access","file_size":1754418,"content_type":"application/pdf","creator":"cziletti"}],"oa_version":"Published Version","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"8014","intvolume":" 101","ddc":["570"],"title":"Neural mechanisms of attending to items in working memory","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"01","date_published":"2019-06-01T00:00:00Z","citation":{"ama":"Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 2019;101:1-12. doi:10.1016/j.neubiorev.2019.03.017","ista":"Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. 2019. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 101, 1–12.","ieee":"S. G. Manohar, N. Zokaei, S. J. Fallon, T. P. Vogels, and M. Husain, “Neural mechanisms of attending to items in working memory,” Neuroscience and Biobehavioral Reviews, vol. 101. Elsevier , pp. 1–12, 2019.","apa":"Manohar, S. G., Zokaei, N., Fallon, S. J., Vogels, T. P., & Husain, M. (2019). Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. Elsevier . https://doi.org/10.1016/j.neubiorev.2019.03.017","mla":"Manohar, Sanjay G., et al. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews, vol. 101, Elsevier , 2019, pp. 1–12, doi:10.1016/j.neubiorev.2019.03.017.","short":"S.G. Manohar, N. Zokaei, S.J. Fallon, T.P. Vogels, M. Husain, Neuroscience and Biobehavioral Reviews 101 (2019) 1–12.","chicago":"Manohar, Sanjay G., Nahid Zokaei, Sean J. Fallon, Tim P Vogels, and Masud Husain. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews. Elsevier , 2019. https://doi.org/10.1016/j.neubiorev.2019.03.017."},"publication":"Neuroscience and Biobehavioral Reviews","page":"1-12","article_type":"original"},{"date_published":"2019-07-01T00:00:00Z","publication":"Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics","citation":{"ama":"Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young diagrams via free boundaries. In: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics; 2019.","ista":"Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew Young diagrams via free boundaries. Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics, 34.","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of skew Young diagrams via free boundaries,” in Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Ljubljana, Slovenia, 2019.","apa":"Betea, D., Bouttier, J., Nejjar, P., & Vuletíc, M. (2019). New edge asymptotics of skew Young diagrams via free boundaries. In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Ljubljana, Slovenia: Formal Power Series and Algebraic Combinatorics.","mla":"Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, 34, Formal Power Series and Algebraic Combinatorics, 2019.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Formal Power Series and Algebraic Combinatorics, 2019.","chicago":"Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics, 2019."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8175","status":"public","title":"New edge asymptotics of skew Young diagrams via free boundaries","abstract":[{"lang":"eng","text":"We study edge asymptotics of poissonized Plancherel-type measures on skew Young diagrams (integer partitions). These measures can be seen as generalizations of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's problem on longest increasing subsequences of random permutations and the last passage percolation (corner growth) discrete versions thereof. Moreover they interpolate between said measures and the uniform measure on partitions. In the new KPZ-like 1/3 exponent edge scaling limit with logarithmic corrections, we find new probability distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions from the theory of random matrices."}],"type":"conference","conference":{"name":"FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics","location":"Ljubljana, Slovenia","start_date":"2019-07-01","end_date":"2019-07-05"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1902.08750","open_access":"1"}],"external_id":{"arxiv":["1902.08750"]},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"month":"07","author":[{"full_name":"Betea, Dan","first_name":"Dan","last_name":"Betea"},{"full_name":"Bouttier, Jérémie","first_name":"Jérémie","last_name":"Bouttier"},{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Nejjar","full_name":"Nejjar, Peter"},{"full_name":"Vuletíc, Mirjana","last_name":"Vuletíc","first_name":"Mirjana"}],"date_updated":"2021-01-12T08:17:18Z","date_created":"2020-07-26T22:01:04Z","year":"2019","acknowledgement":"D.B. is especially grateful to Patrik Ferrari for suggesting simplifications in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models of Section 2.\r\n","publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Formal Power Series and Algebraic Combinatorics","ec_funded":1,"article_number":"34"},{"title":"AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice","status":"public","intvolume":" 12","_id":"8228","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Background: Atopics have a lower risk for malignancies, and IgE targeted to tumors is superior to IgG in fighting cancer. Whether IgE-mediated innate or adaptive immune surveillance can confer protection against tumors remains unclear.\r\nObjective: We aimed to investigate the effects of active and passive immunotherapy to the tumor-associated antigen HER-2 in three murine models differing in Epsilon-B-cell-receptor expression affecting the levels of expressed IgE.\r\nMethods: We compared the levels of several serum specific anti-HER-2 antibodies (IgE, IgG1, IgG2a, IgG2b, IgA) and the survival rates in low-IgE ΔM1M2 mice lacking the transmembrane/cytoplasmic domain of Epsilon-B-cell-receptors expressing reduced IgE levels, high-IgE KN1 mice expressing chimeric Epsilon-Gamma1-B-cell receptors with 4-6-fold elevated serum IgE levels, and wild type (WT) BALB/c. Prior engrafting mice with D2F2/E2 mammary tumors overexpressing HER-2, mice were vaccinated with HER-2 or vehicle control PBS using the Th2-adjuvant Al(OH)3 (active immunotherapy), or treated with the murine anti-HER-2 IgG1 antibody 4D5 (passive immunotherapy).\r\nResults: Overall, among the three strains of mice, HER-2 vaccination induced significantly higher levels of HER-2 specific IgE and IgG1 in high-IgE KN1, while low-IgE ΔM1M2 mice had higher IgG2a levels. HER-2 vaccination and passive immunotherapy prolonged the survival in tumor-grafted WT and low-IgE ΔM1M2 strains compared with treatment controls; active vaccination provided the highest benefit. Notably, untreated high-IgE KN1 mice displayed the longest survival of all strains, which could not be further extended by active or passive immunotherapy.\r\nConclusion: Active and passive immunotherapies prolong survival in wild type and low-IgE ΔM1M2 mice engrafted with mammary tumors. High-IgE KN1 mice have an innate survival benefit following tumor challenge.","lang":"eng"}],"issue":"7","article_type":"original","publication":"World Allergy Organization Journal","citation":{"mla":"Singer, Josef, et al. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal, vol. 12, no. 7, 100044, Elsevier, 2019, doi:10.1016/j.waojou.2019.100044.","short":"J. Singer, G. Achatz-Straussberger, A. Bentley-Lukschal, J. Singer, G. Achatz, S.N. Karagiannis, E. Jensen-Jarolim, World Allergy Organization Journal 12 (2019).","chicago":"Singer, Josef, Gertrude Achatz-Straussberger, Anna Bentley-Lukschal, Judit Singer, Gernot Achatz, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal. Elsevier, 2019. https://doi.org/10.1016/j.waojou.2019.100044.","ama":"Singer J, Achatz-Straussberger G, Bentley-Lukschal A, et al. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 2019;12(7). doi:10.1016/j.waojou.2019.100044","ista":"Singer J, Achatz-Straussberger G, Bentley-Lukschal A, Singer J, Achatz G, Karagiannis SN, Jensen-Jarolim E. 2019. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 12(7), 100044.","apa":"Singer, J., Achatz-Straussberger, G., Bentley-Lukschal, A., Singer, J., Achatz, G., Karagiannis, S. N., & Jensen-Jarolim, E. (2019). AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. Elsevier. https://doi.org/10.1016/j.waojou.2019.100044","ieee":"J. Singer et al., “AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice,” World Allergy Organization Journal, vol. 12, no. 7. Elsevier, 2019."},"date_published":"2019-07-29T00:00:00Z","day":"29","article_processing_charge":"No","publication_status":"published","publisher":"Elsevier","year":"2019","date_created":"2020-08-10T11:50:54Z","date_updated":"2021-01-12T08:17:36Z","volume":12,"author":[{"full_name":"Singer, Josef","first_name":"Josef","last_name":"Singer","orcid":"0000-0002-8701-2412"},{"full_name":"Achatz-Straussberger, Gertrude","last_name":"Achatz-Straussberger","first_name":"Gertrude"},{"full_name":"Bentley-Lukschal, Anna","first_name":"Anna","last_name":"Bentley-Lukschal"},{"full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","first_name":"Judit","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Achatz, Gernot","first_name":"Gernot","last_name":"Achatz"},{"full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis","first_name":"Sophia N."},{"first_name":"Erika","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika"}],"article_number":"100044","extern":"1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.waojou.2019.100044","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.waojou.2019.100044","month":"07","publication_identifier":{"issn":["1939-4551"]}},{"month":"10","publication_identifier":{"issn":["2072-6643"]},"language":[{"iso":"eng"}],"doi":"10.3390/nu11102463","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.3390/nu11102463","open_access":"1"}],"oa":1,"extern":"1","article_number":"2463","date_updated":"2021-01-12T08:17:36Z","date_created":"2020-08-10T11:51:04Z","volume":11,"author":[{"full_name":"Ondracek, Anna S.","last_name":"Ondracek","first_name":"Anna S.","orcid":"0000-0001-7625-3651"},{"last_name":"Heiden","first_name":"Denise","full_name":"Heiden, Denise"},{"first_name":"Gertie J.","last_name":"Oostingh","full_name":"Oostingh, Gertie J."},{"full_name":"Fuerst, Elisabeth","last_name":"Fuerst","first_name":"Elisabeth"},{"first_name":"Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit"},{"full_name":"Bergmayr, Cornelia","first_name":"Cornelia","last_name":"Bergmayr"},{"full_name":"Rohrhofer, Johanna","orcid":"0000-0002-2783-2099","first_name":"Johanna","last_name":"Rohrhofer"},{"first_name":"Erika","last_name":"Jensen-Jarolim","orcid":"0000-0003-4019-5765","full_name":"Jensen-Jarolim, Erika"},{"orcid":"0000-0002-7034-9860","first_name":"Albert","last_name":"Duschl","full_name":"Duschl, Albert"},{"full_name":"Untersmayr, Eva","last_name":"Untersmayr","first_name":"Eva","orcid":"0000-0002-1963-499X"}],"publication_status":"published","publisher":"MDPI","year":"2019","day":"15","article_processing_charge":"No","date_published":"2019-10-15T00:00:00Z","article_type":"original","publication":"Nutrients","citation":{"ieee":"A. S. Ondracek et al., “Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model,” Nutrients, vol. 11, no. 10. MDPI, 2019.","apa":"Ondracek, A. S., Heiden, D., Oostingh, G. J., Fuerst, E., Singer, J., Bergmayr, C., … Untersmayr, E. (2019). Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. MDPI. https://doi.org/10.3390/nu11102463","ista":"Ondracek AS, Heiden D, Oostingh GJ, Fuerst E, Singer J, Bergmayr C, Rohrhofer J, Jensen-Jarolim E, Duschl A, Untersmayr E. 2019. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 11(10), 2463.","ama":"Ondracek AS, Heiden D, Oostingh GJ, et al. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 2019;11(10). doi:10.3390/nu11102463","chicago":"Ondracek, Anna S., Denise Heiden, Gertie J. Oostingh, Elisabeth Fuerst, Judit Singer, Cornelia Bergmayr, Johanna Rohrhofer, Erika Jensen-Jarolim, Albert Duschl, and Eva Untersmayr. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients. MDPI, 2019. https://doi.org/10.3390/nu11102463.","short":"A.S. Ondracek, D. Heiden, G.J. Oostingh, E. Fuerst, J. Singer, C. Bergmayr, J. Rohrhofer, E. Jensen-Jarolim, A. Duschl, E. Untersmayr, Nutrients 11 (2019).","mla":"Ondracek, Anna S., et al. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients, vol. 11, no. 10, 2463, MDPI, 2019, doi:10.3390/nu11102463."},"abstract":[{"text":"Food proteins may get nitrated by various exogenous or endogenous mechanisms. As individuals might get recurrently exposed to nitrated proteins via daily diet, we aimed to investigate the effect of repeatedly ingested nitrated food proteins on the subsequent immune response in non-allergic and allergic mice using the milk allergen beta-lactoglobulin (BLG) as model food protein in a mouse model. Evaluating the presence of nitrated proteins in food, we could detect 3-nitrotyrosine (3-NT) in extracts of different foods and in stomach content extracts of non-allergic mice under physiological conditions. Chemically nitrated BLG (BLGn) exhibited enhanced susceptibility to degradation in simulated gastric fluid experiments compared to untreated BLG (BLGu). Gavage of BLGn to non-allergic animals increased interferon-γ and interleukin-10 release of stimulated spleen cells and led to the formation of BLG-specific serum IgA. Allergic mice receiving three oral gavages of BLGn had higher levels of mouse mast cell protease-1 (mMCP-1) compared to allergic mice receiving BLGu. Regardless of the preceding immune status, non-allergic or allergic, repeatedly ingested nitrated food proteins seem to considerably influence the subsequent immune response.","lang":"eng"}],"issue":"10","type":"journal_article","oa_version":"Published Version","status":"public","title":"Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model","intvolume":" 11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8229"},{"extern":"1","issue":"10","type":"journal_article","oa_version":"Published Version","volume":74,"date_updated":"2021-01-12T08:17:35Z","date_created":"2020-08-10T11:50:42Z","author":[{"last_name":"Ilieva","first_name":"Kristina M.","full_name":"Ilieva, Kristina M."},{"orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas-Singer","first_name":"Judit","full_name":"Fazekas-Singer, Judit"},{"full_name":"Bax, Heather J.","first_name":"Heather J.","last_name":"Bax"},{"full_name":"Crescioli, Silvia","first_name":"Silvia","last_name":"Crescioli"},{"last_name":"Montero‐Morales","first_name":"Laura","full_name":"Montero‐Morales, Laura"},{"first_name":"Silvia","last_name":"Mele","full_name":"Mele, Silvia"},{"last_name":"Sow","first_name":"Heng Sheng","full_name":"Sow, Heng Sheng"},{"full_name":"Stavraka, Chara","last_name":"Stavraka","first_name":"Chara"},{"full_name":"Josephs, Debra H.","last_name":"Josephs","first_name":"Debra H."},{"first_name":"James F.","last_name":"Spicer","full_name":"Spicer, James F."},{"full_name":"Steinkellner, Herta","orcid":"0000-0003-4823-1505","first_name":"Herta","last_name":"Steinkellner"},{"orcid":"0000-0003-4019-5765","first_name":"Erika","last_name":"Jensen‐Jarolim","full_name":"Jensen‐Jarolim, Erika"},{"full_name":"Tutt, Andrew N. J.","last_name":"Tutt","first_name":"Andrew N. J.","orcid":"0000-0001-8715-2901"},{"orcid":"0000-0002-4100-7810","last_name":"Karagiannis","first_name":"Sophia N.","full_name":"Karagiannis, Sophia N."}],"intvolume":" 74","publisher":"Wiley","publication_status":"published","title":"AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8227","year":"2019","publication_identifier":{"issn":["0105-4538","1398-9995"]},"article_processing_charge":"No","month":"10","day":"01","language":[{"iso":"eng"}],"doi":"10.1111/all.13818","date_published":"2019-10-01T00:00:00Z","page":"1985-1989","quality_controlled":"1","article_type":"letter_note","oa":1,"citation":{"chicago":"Ilieva, Kristina M., Judit Singer, Heather J. Bax, Silvia Crescioli, Laura Montero‐Morales, Silvia Mele, Heng Sheng Sow, et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy. Wiley, 2019. https://doi.org/10.1111/all.13818.","short":"K.M. Ilieva, J. Singer, H.J. Bax, S. Crescioli, L. Montero‐Morales, S. Mele, H.S. Sow, C. Stavraka, D.H. Josephs, J.F. Spicer, H. Steinkellner, E. Jensen‐Jarolim, A.N.J. Tutt, S.N. Karagiannis, Allergy 74 (2019) 1985–1989.","mla":"Ilieva, Kristina M., et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy, vol. 74, no. 10, Wiley, 2019, pp. 1985–89, doi:10.1111/all.13818.","ieee":"K. M. Ilieva et al., “AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody,” Allergy, vol. 74, no. 10. Wiley, pp. 1985–1989, 2019.","apa":"Ilieva, K. M., Singer, J., Bax, H. J., Crescioli, S., Montero‐Morales, L., Mele, S., … Karagiannis, S. N. (2019). AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. Wiley. https://doi.org/10.1111/all.13818","ista":"Ilieva KM, Singer J, Bax HJ, Crescioli S, Montero‐Morales L, Mele S, Sow HS, Stavraka C, Josephs DH, Spicer JF, Steinkellner H, Jensen‐Jarolim E, Tutt ANJ, Karagiannis SN. 2019. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 74(10), 1985–1989.","ama":"Ilieva KM, Singer J, Bax HJ, et al. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 2019;74(10):1985-1989. doi:10.1111/all.13818"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/all.13818"}],"publication":"Allergy"},{"type":"journal_article","article_number":"83","abstract":[{"lang":"eng","text":"Background: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.\r\n\r\nResults: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions.\r\nThe total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.\r\nMapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.\r\n\r\nConclusions: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8263","year":"2019","intvolume":" 19","publisher":"Springer Nature","status":"public","title":"Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow","publication_status":"published","author":[{"full_name":"Shelyakin, Pavel V.","orcid":"0000-0003-0120-9319","first_name":"Pavel V.","last_name":"Shelyakin"},{"full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"first_name":"Anna A.","last_name":"Karan","full_name":"Karan, Anna A."},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"volume":19,"oa_version":"Published Version","date_updated":"2023-02-23T13:28:54Z","date_created":"2020-08-15T11:04:07Z","article_processing_charge":"No","publication_identifier":{"issn":["1471-2148"]},"month":"03","day":"27","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12862-019-1403-6"}],"citation":{"ama":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 2019;19. doi:10.1186/s12862-019-1403-6","ista":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. 2019. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 19, 83.","ieee":"P. V. Shelyakin, O. Bochkareva, A. A. Karan, and M. S. Gelfand, “Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow,” BMC Evolutionary Biology, vol. 19. Springer Nature, 2019.","apa":"Shelyakin, P. V., Bochkareva, O., Karan, A. A., & Gelfand, M. S. (2019). Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. Springer Nature. https://doi.org/10.1186/s12862-019-1403-6","mla":"Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology, vol. 19, 83, Springer Nature, 2019, doi:10.1186/s12862-019-1403-6.","short":"P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary Biology 19 (2019).","chicago":"Shelyakin, Pavel V., Olga Bochkareva, Anna A. Karan, and Mikhail S. Gelfand. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology. Springer Nature, 2019. https://doi.org/10.1186/s12862-019-1403-6."},"oa":1,"publication":"BMC Evolutionary Biology","quality_controlled":"1","article_type":"original","date_published":"2019-03-27T00:00:00Z","doi":"10.1186/s12862-019-1403-6","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"While showing great promise, smart contracts are difficult to program correctly, as they need a deep understanding of cryptography and distributed algorithms, and offer limited functionality, as they have to be deterministic and cannot operate on secret data. In this paper we present Protean, a general-purpose decentralized computing platform that addresses these limitations by moving from a monolithic execution model, where all participating nodes store all the state and execute every computation, to a modular execution-model. Protean employs secure specialized modules, called functional units, for building decentralized applications that are currently insecure or impossible to implement with smart contracts. Each functional unit is a distributed system that provides a special-purpose functionality by exposing atomic transactions to the smart-contract developer. Combining these transactions into arbitrarily-defined workflows, developers can build a larger class of decentralized applications, such as provably-secure and fair lotteries or e-voting."}],"extern":"1","type":"conference","author":[{"full_name":"Alp, Enis Ceyhun","last_name":"Alp","first_name":"Enis Ceyhun"},{"first_name":"Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Fragkouli, Georgia","first_name":"Georgia","last_name":"Fragkouli"},{"full_name":"Ford, Bryan","last_name":"Ford","first_name":"Bryan"}],"oa_version":"None","date_updated":"2021-01-12T08:17:56Z","date_created":"2020-08-26T11:45:45Z","year":"2019","_id":"8296","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","publication_status":"published","title":"Rethinking general-purpose decentralized computing","status":"public","publication_identifier":{"isbn":["9781450367271"]},"article_processing_charge":"No","month":"05","day":"01","scopus_import":"1","date_published":"2019-05-01T00:00:00Z","doi":"10.1145/3317550.3321448","conference":{"name":"HotOS: Workshop on Hot Topics in Operating Systems","end_date":"2019-05-15","start_date":"2019-05-13","location":"Bertinoro, Italy"},"language":[{"iso":"eng"}],"citation":{"ista":"Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. 2019. Rethinking general-purpose decentralized computing. Proceedings of the Workshop on Hot Topics in Operating Systems. HotOS: Workshop on Hot Topics in Operating Systems, 105–112.","apa":"Alp, E. C., Kokoris Kogias, E., Fragkouli, G., & Ford, B. (2019). Rethinking general-purpose decentralized computing. In Proceedings of the Workshop on Hot Topics in Operating Systems (pp. 105–112). Bertinoro, Italy: ACM. https://doi.org/10.1145/3317550.3321448","ieee":"E. C. Alp, E. Kokoris Kogias, G. Fragkouli, and B. Ford, “Rethinking general-purpose decentralized computing,” in Proceedings of the Workshop on Hot Topics in Operating Systems, Bertinoro, Italy, 2019, pp. 105–112.","ama":"Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. Rethinking general-purpose decentralized computing. In: Proceedings of the Workshop on Hot Topics in Operating Systems. ACM; 2019:105-112. doi:10.1145/3317550.3321448","chicago":"Alp, Enis Ceyhun, Eleftherios Kokoris Kogias, Georgia Fragkouli, and Bryan Ford. “Rethinking General-Purpose Decentralized Computing.” In Proceedings of the Workshop on Hot Topics in Operating Systems, 105–12. ACM, 2019. https://doi.org/10.1145/3317550.3321448.","mla":"Alp, Enis Ceyhun, et al. “Rethinking General-Purpose Decentralized Computing.” Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–12, doi:10.1145/3317550.3321448.","short":"E.C. Alp, E. Kokoris Kogias, G. Fragkouli, B. Ford, in:, Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–112."},"publication":"Proceedings of the Workshop on Hot Topics in Operating Systems","page":"105-112","quality_controlled":"1"},{"publication_status":"submitted","status":"public","title":"SoK: Communication across distributed ledgers","_id":"8304","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2019","oa_version":"Preprint","date_created":"2020-08-26T12:16:38Z","date_updated":"2021-09-24T12:08:14Z","author":[{"full_name":"Zamyatin, Alexei","first_name":"Alexei","last_name":"Zamyatin"},{"full_name":"Al-Bassam, Mustafa","first_name":"Mustafa","last_name":"Al-Bassam"},{"full_name":"Zindros, Dionysis","first_name":"Dionysis","last_name":"Zindros"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"last_name":"Moreno-Sanchez","first_name":"Pedro","full_name":"Moreno-Sanchez, Pedro"},{"first_name":"Aggelos","last_name":"Kiayias","full_name":"Kiayias, Aggelos"},{"full_name":"Knottenbelt, William J.","first_name":"William J.","last_name":"Knottenbelt"}],"type":"preprint","article_number":"2019/1128","extern":"1","abstract":[{"lang":"eng","text":"Enabling secure communication across distributed systems is usually studied under the assumption of trust between the different systems and an external adversary trying to compromise the messages. With the appearance of distributed ledgers or blockchains, numerous protocols have emerged, which attempt to achieve trustless communication between distrusting ledgers and participants. Cross-chain communication (CCC) thereby plays a fundamental role in cryptocurrency exchanges, sharding, bootstrapping of new and feature-extension of existing distributed ledgers. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence on their correctness and composability.\r\nWe provide the first systematic exposition of protocols for CCC. First, we formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. We then develop a framework to evaluate existing and to design new cross-chain protocols. The framework is based on the use case, the trust model, and the security assumptions of interlinked blockchains. Finally, we identify security and privacy challenges faced by protocols in the cross-chain setting.\r\nThis Systematization of Knowledge (SoK) offers a comprehensive guide for designing protocols bridging the numerous distributed ledgers available today. It aims to facilitate clearer communication between academia and industry in the field."}],"oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2019/1128 ","open_access":"1"}],"citation":{"ista":"Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. SoK: Communication across distributed ledgers. Cryptology ePrint Archive, 2019/1128.","apa":"Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (n.d.). SoK: Communication across distributed ledgers. Cryptology ePrint Archive.","ieee":"A. Zamyatin et al., “SoK: Communication across distributed ledgers,” Cryptology ePrint Archive. .","ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. Cryptology ePrint Archive.","chicago":"Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, n.d.","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, 2019/1128.","short":"A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, Cryptology EPrint Archive (n.d.)."},"publication":"Cryptology ePrint Archive","language":[{"iso":"eng"}],"date_published":"2019-10-01T00:00:00Z","article_processing_charge":"No","month":"10","day":"01"},{"article_processing_charge":"No","month":"06","day":"06","oa":1,"citation":{"chicago":"Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, n.d.","short":"E. Kokoris Kogias, Cryptology EPrint Archive (n.d.).","mla":"Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, 2019/676.","ieee":"E. Kokoris Kogias, “Robust and scalable consensus for sharded distributed ledgers,” Cryptology ePrint Archive. .","apa":"Kokoris Kogias, E. (n.d.). Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive.","ista":"Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive, 2019/676.","ama":"Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive."},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/676"}],"publication":"Cryptology ePrint Archive","date_published":"2019-06-06T00:00:00Z","language":[{"iso":"eng"}],"type":"preprint","article_number":"2019/676","abstract":[{"text":"ByzCoin, a promising alternative of Bitcoin, is a scalable consensus protocol used as a building block of many research and enterprise-level decentralized systems. In this paper, we show that ByzCoin is unsuitable for deployment in an anopen, adversarial network and instead introduceMOTOR. MOTORis designed as a secure, robust, and scalable consensus suitable for permissionless sharded blockchains. MOTORachieves these properties by making four key design choices: (a) it prioritizes robustness in adversarial environments while maintaining adequate scalability, (b) it employees provably correct cryptography that resists DoS attacks from individual nodes, (c) it deploys unpredictable rotating leaders to defend against mildly-adaptive adversaries and prevents censorship, and (d) it creates an incentive compatible reward mechanism. These choices are materialized as (a) a “rotating subleader” communication pattern that balances the scalability needs with the robustness requirements under failures, (b) deployment of provable secure BLS multi-signatures, (c) use of deterministic thresh-old signatures as a source of randomness and (d) careful design of the reward allocation mechanism. We have implemented MOTORand compare it withByzCoin. We show that MOTORcan scale similar to ByzCoin with an at most2xoverhead whereas it maintains good performance even under high-percentage of faults, unlike ByzCoin.","lang":"eng"}],"extern":"1","year":"2019","_id":"8303","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"submitted","status":"public","title":"Robust and scalable consensus for sharded distributed ledgers","author":[{"last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"}],"oa_version":"Preprint","date_updated":"2021-09-24T12:07:11Z","date_created":"2020-08-26T12:13:56Z"},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.5075/epfl-thesis-7101"}],"citation":{"mla":"Kokoris Kogias, Eleftherios. Secure, Confidential Blockchains Providing High Throughput and Low Latency. École Polytechnique Fédérale de Lausanne, 2019, doi:10.5075/epfl-thesis-7101.","short":"E. Kokoris Kogias, Secure, Confidential Blockchains Providing High Throughput and Low Latency, École Polytechnique Fédérale de Lausanne, 2019.","chicago":"Kokoris Kogias, Eleftherios. “Secure, Confidential Blockchains Providing High Throughput and Low Latency.” École Polytechnique Fédérale de Lausanne, 2019. https://doi.org/10.5075/epfl-thesis-7101.","ama":"Kokoris Kogias E. Secure, confidential blockchains providing high throughput and low latency. 2019. doi:10.5075/epfl-thesis-7101","ista":"Kokoris Kogias E. 2019. Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne.","apa":"Kokoris Kogias, E. (2019). Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne. https://doi.org/10.5075/epfl-thesis-7101","ieee":"E. Kokoris Kogias, “Secure, confidential blockchains providing high throughput and low latency,” École Polytechnique Fédérale de Lausanne, 2019."},"page":"244","doi":"10.5075/epfl-thesis-7101","date_published":"2019-09-27T00:00:00Z","degree_awarded":"PhD","supervisor":[{"full_name":"Ford, Bryan Alexander","first_name":"Bryan Alexander","last_name":"Ford"}],"language":[{"iso":"eng"}],"day":"27","month":"09","article_processing_charge":"No","year":"2019","_id":"8311","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Secure, confidential blockchains providing high throughput and low latency","publication_status":"published","status":"public","publisher":"École Polytechnique Fédérale de Lausanne","author":[{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"}],"date_updated":"2021-12-20T15:30:47Z","date_created":"2020-08-27T11:22:24Z","oa_version":"Published Version","type":"dissertation","abstract":[{"lang":"eng","text":"One of the core promises of blockchain technology is that of enabling trustworthy data dissemination in a trustless environment. What current blockchain systems deliver, however, is slow dissemination of public data, rendering blockchain technology unusable in settings where latency, transaction capacity, or data confidentiality are important. In this thesis we focus on providing solutions on two of the most pressing problems blockchain technology currently faces: scalability and data confidentiality. To address the scalability issue, we present OMNILEDGER, a novel scale-out distributed ledger that preserves long-term security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient cross-shard commit protocol that atomically handles transactions affecting multiple shards. To enable secure sharing of confidential data we present CALYPSO, the first fully decentralized, auditable access-control framework for secure blockchain-based data sharing which builds upon two abstractions. First, on-chain secrets enable collective management of (verifiably shared) secrets under a Byzantine adversary where an access-control blockchain enforces user-specific access rules and a secret-management cothority administers encrypted data. Second, skipchain-based identity and access management enables efficient administration of dynamic, sovereign identities and access policies and, in particular, permits clients to maintain long-term relationships with respect to evolving user identities thanks to the trust-delegating forward links of skipchains. In order to build OMNILEDGER and CALYPSO, we first build a set of tools for efficient decentralization, which are presented in Part II of this dissertation. These tools can be used in decentralized and distributed systems to achieve (1) scalable consensus (BYZCOIN), (2) bias- resistant distributed randomness creations (RANDHOUND), and (3) relationship-keeping between independently updating communication endpoints (SKIPCHAINIAC). Although we use this tools in the scope off this thesis, they can be (and already have been) used in a far wider scope."}],"extern":"1"},{"publication":"arXiv","oa":1,"citation":{"mla":"Avarikioti, Georgia, et al. “Brick: Asynchronous Payment Channels.” ArXiv, 1905.11360.","short":"G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, ArXiv (n.d.).","chicago":"Avarikioti, Georgia, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Payment Channels.” ArXiv, n.d.","ama":"Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. arXiv.","ista":"Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. arXiv, 1905.11360.","apa":"Avarikioti, G., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (n.d.). Brick: Asynchronous payment channels. arXiv.","ieee":"G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous payment channels,” arXiv. ."},"external_id":{"arxiv":["1905.11360"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.11360"}],"language":[{"iso":"eng"}],"date_published":"2019-05-27T00:00:00Z","month":"05","day":"27","article_processing_charge":"No","publication_status":"submitted","title":"Brick: Asynchronous payment channels","status":"public","_id":"8314","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-27T11:36:54Z","date_updated":"2021-01-12T08:18:04Z","oa_version":"Preprint","author":[{"last_name":"Avarikioti","first_name":"Georgia","full_name":"Avarikioti, Georgia"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Wattenhofer, Roger","first_name":"Roger","last_name":"Wattenhofer"},{"last_name":"Zindros","first_name":"Dionysis","full_name":"Zindros, Dionysis"}],"article_number":"1905.11360","type":"preprint","extern":"1","abstract":[{"text":"Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called Wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee's approval for the last valid state. Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead,\r\nBrick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. Furthermore, we consider permissioned blockchains, where the additional property of auditability might be desired for regulatory purposes. We introduce Brick+, an off-chain construction that provides auditability on top of Brick without conflicting with its privacy guarantees. We formally define the properties our payment channel construction should fulfill, and prove that both Brick and Brick+ satisfy them. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity.","lang":"eng"}]},{"date_published":"2019-10-23T00:00:00Z","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1910.10434","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1910.10434"]},"citation":{"ieee":"G. Avarikioti, E. Kokoris Kogias, and R. Wattenhofer, “Divide and scale: Formalization of distributed ledger sharding protocols,” arXiv. .","apa":"Avarikioti, G., Kokoris Kogias, E., & Wattenhofer, R. (n.d.). Divide and scale: Formalization of distributed ledger sharding protocols. arXiv.","ista":"Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. arXiv, 1910.10434.","ama":"Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. arXiv.","chicago":"Avarikioti, Georgia, Eleftherios Kokoris Kogias, and Roger Wattenhofer. “Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv, n.d.","short":"G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, ArXiv (n.d.).","mla":"Avarikioti, Georgia, et al. “Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv, 1910.10434."},"publication":"arXiv","article_processing_charge":"No","day":"23","month":"10","author":[{"first_name":"Georgia","last_name":"Avarikioti","full_name":"Avarikioti, Georgia"},{"last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios"},{"last_name":"Wattenhofer","first_name":"Roger","full_name":"Wattenhofer, Roger"}],"oa_version":"Preprint","date_updated":"2021-01-12T08:18:05Z","date_created":"2020-08-27T11:37:43Z","year":"2019","_id":"8315","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Divide and scale: Formalization of distributed ledger sharding protocols","publication_status":"submitted","abstract":[{"text":"Sharding distributed ledgers is the most promising on-chain solution for scaling blockchain technology. In this work, we define and analyze the properties a sharded distributed ledger should fulfill. More specifically, we show that a sharded blockchain cannot be scalable under a fully adaptive adversary, but it can scale up to $O(n/\\log n)$ under an epoch-adaptive adversary. This is possible only if the distributed ledger creates succinct proofs of the valid state updates at the end of each epoch. Our model builds upon and extends the Bitcoin backbone protocol by defining consistency and\r\nscalability. Consistency encompasses the need for atomic execution of cross-shard transactions to preserve safety, whereas scalability encapsulates the speedup a sharded system can gain in comparison to a non-sharded system. In\r\norder to show the power of our framework, we analyze the most prominent sharded blockchains and either prove their correctness (OmniLedger, RapidChain) under our model or pinpoint where they fail to balance the consistency and\r\nscalability requirements (Elastico, Monoxide). ","lang":"eng"}],"extern":"1","type":"preprint","article_number":"1910.10434"},{"date_published":"2019-08-22T00:00:00Z","citation":{"mla":"Ford, Bryan, et al. Methods and Systems for Secure Data Exchange. 2019.","short":"B. Ford, L. Gasser, E. Kokoris Kogias, P. Janovic, (2019).","chicago":"Ford, Bryan, Linus Gasser, Eleftherios Kokoris Kogias, and Philipp Janovic. “Methods and Systems for Secure Data Exchange,” 2019.","ama":"Ford B, Gasser L, Kokoris Kogias E, Janovic P. Methods and systems for secure data exchange. 2019.","ista":"Ford B, Gasser L, Kokoris Kogias E, Janovic P. 2019. Methods and systems for secure data exchange.","ieee":"B. Ford, L. Gasser, E. Kokoris Kogias, and P. Janovic, “Methods and systems for secure data exchange.” 2019.","apa":"Ford, B., Gasser, L., Kokoris Kogias, E., & Janovic, P. (2019). Methods and systems for secure data exchange."},"ipn":"WO2019158209 (A1)","publication_date":"2019-08-22","oa":1,"main_file_link":[{"url":"https://patents.google.com/patent/WO2019158209A1","open_access":"1"}],"day":"22","month":"08","article_processing_charge":"No","date_updated":"2022-01-05T14:00:32Z","date_created":"2020-08-27T11:24:44Z","ipc":"G06F21/62 ; H04L9/08 ; H04L9/32","oa_version":"Published Version","author":[{"full_name":"Ford, Bryan","first_name":"Bryan","last_name":"Ford"},{"first_name":"Linus","last_name":"Gasser","full_name":"Gasser, Linus"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias"},{"full_name":"Janovic, Philipp","last_name":"Janovic","first_name":"Philipp"}],"title":"Methods and systems for secure data exchange","status":"public","applicant":["École Polytechnique Fédérale De Lausanne "],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"8313","year":"2019","extern":"1","abstract":[{"text":"The present invention concerns a computer-implemented method for secure data exchange between a sender (A) and a recipient (B), wherein the method is performed by the sender (A) and comprises encrypting data using a symmetric key k, creating a write transaction T W , wherein the write transaction T W comprises information usable to derive the symmetric key k and an access policy identifying the recipient (B) as being allowed to decrypt the encrypted data, providing the recipient (B) access to the encrypted data, and sending the write transaction T W to a first group of servers (AC) for being stored in a blockchain data structure maintained by the first group of servers (AC).","lang":"eng"}],"type":"patent"},{"extern":"1","article_number":"2697","volume":10,"date_updated":"2021-01-12T08:19:03Z","date_created":"2020-09-17T10:28:25Z","author":[{"full_name":"Gauto, Diego F.","last_name":"Gauto","first_name":"Diego F."},{"full_name":"Estrozi, Leandro F.","last_name":"Estrozi","first_name":"Leandro F."},{"full_name":"Schwieters, Charles D.","first_name":"Charles D.","last_name":"Schwieters"},{"full_name":"Effantin, Gregory","last_name":"Effantin","first_name":"Gregory"},{"full_name":"Macek, Pavel","last_name":"Macek","first_name":"Pavel"},{"first_name":"Remy","last_name":"Sounier","full_name":"Sounier, Remy"},{"last_name":"Sivertsen","first_name":"Astrid C.","full_name":"Sivertsen, Astrid C."},{"last_name":"Schmidt","first_name":"Elena","full_name":"Schmidt, Elena"},{"full_name":"Kerfah, Rime","first_name":"Rime","last_name":"Kerfah"},{"first_name":"Guillaume","last_name":"Mas","full_name":"Mas, Guillaume"},{"first_name":"Jacques-Philippe","last_name":"Colletier","full_name":"Colletier, Jacques-Philippe"},{"full_name":"Güntert, Peter","last_name":"Güntert","first_name":"Peter"},{"full_name":"Favier, Adrien","first_name":"Adrien","last_name":"Favier"},{"first_name":"Guy","last_name":"Schoehn","full_name":"Schoehn, Guy"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda"},{"full_name":"Boisbouvier, Jerome","last_name":"Boisbouvier","first_name":"Jerome"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"year":"2019","publication_identifier":{"issn":["2041-1723"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-10490-9","quality_controlled":"1","external_id":{"pmid":["31217444"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-019-10490-9"}],"abstract":[{"lang":"eng","text":"Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 10","status":"public","title":"Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8405","article_processing_charge":"No","day":"19","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"date_published":"2019-06-19T00:00:00Z","article_type":"original","citation":{"apa":"Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier, R., … Boisbouvier, J. (2019). Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-10490-9","ieee":"D. F. Gauto et al., “Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex,” Nature Communications, vol. 10. Springer Nature, 2019.","ista":"Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier J-P, Güntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J. 2019. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 10, 2697.","ama":"Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 2019;10. doi:10.1038/s41467-019-10490-9","chicago":"Gauto, Diego F., Leandro F. Estrozi, Charles D. Schwieters, Gregory Effantin, Pavel Macek, Remy Sounier, Astrid C. Sivertsen, et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-10490-9.","short":"D.F. Gauto, L.F. Estrozi, C.D. Schwieters, G. Effantin, P. Macek, R. Sounier, A.C. Sivertsen, E. Schmidt, R. Kerfah, G. Mas, J.-P. Colletier, P. Güntert, A. Favier, G. Schoehn, P. Schanda, J. Boisbouvier, Nature Communications 10 (2019).","mla":"Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications, vol. 10, 2697, Springer Nature, 2019, doi:10.1038/s41467-019-10490-9."},"publication":"Nature Communications"},{"month":"09","publication_identifier":{"issn":["2375-2548"]},"quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.1126/sciadv.aaw3818","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.aaw3818","article_number":"eaaw3818","extern":"1","publication_status":"published","publisher":"American Association for the Advancement of Science","year":"2019","date_created":"2020-09-17T10:28:36Z","date_updated":"2021-01-12T08:19:03Z","volume":5,"author":[{"full_name":"Felix, Jan","first_name":"Jan","last_name":"Felix"},{"full_name":"Weinhäupl, Katharina","first_name":"Katharina","last_name":"Weinhäupl"},{"last_name":"Chipot","first_name":"Christophe","full_name":"Chipot, Christophe"},{"last_name":"Dehez","first_name":"François","full_name":"Dehez, François"},{"last_name":"Hessel","first_name":"Audrey","full_name":"Hessel, Audrey"},{"full_name":"Gauto, Diego F.","first_name":"Diego F.","last_name":"Gauto"},{"last_name":"Morlot","first_name":"Cecile","full_name":"Morlot, Cecile"},{"full_name":"Abian, Olga","last_name":"Abian","first_name":"Olga"},{"last_name":"Gutsche","first_name":"Irina","full_name":"Gutsche, Irina"},{"first_name":"Adrian","last_name":"Velazquez-Campoy","full_name":"Velazquez-Campoy, Adrian"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul"},{"first_name":"Hugo","last_name":"Fraga","full_name":"Fraga, Hugo"}],"day":"04","article_processing_charge":"No","article_type":"original","publication":"Science Advances","citation":{"mla":"Felix, Jan, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances, vol. 5, no. 9, eaaw3818, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw3818.","short":"J. Felix, K. Weinhäupl, C. Chipot, F. Dehez, A. Hessel, D.F. Gauto, C. Morlot, O. Abian, I. Gutsche, A. Velazquez-Campoy, P. Schanda, H. Fraga, Science Advances 5 (2019).","chicago":"Felix, Jan, Katharina Weinhäupl, Christophe Chipot, François Dehez, Audrey Hessel, Diego F. Gauto, Cecile Morlot, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw3818.","ama":"Felix J, Weinhäupl K, Chipot C, et al. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw3818","ista":"Felix J, Weinhäupl K, Chipot C, Dehez F, Hessel A, Gauto DF, Morlot C, Abian O, Gutsche I, Velazquez-Campoy A, Schanda P, Fraga H. 2019. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 5(9), eaaw3818.","ieee":"J. Felix et al., “Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019.","apa":"Felix, J., Weinhäupl, K., Chipot, C., Dehez, F., Hessel, A., Gauto, D. F., … Fraga, H. (2019). Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw3818"},"date_published":"2019-09-04T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation."}],"issue":"9","status":"public","title":"Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors","intvolume":" 5","_id":"8406","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version"},{"external_id":{"pmid":["30620186"]},"quality_controlled":"1","doi":"10.1021/jacs.8b09258","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0002-7863","1520-5126"]},"month":"01","pmid":1,"year":"2019","publisher":"American Chemical Society","publication_status":"published","author":[{"full_name":"Rovó, Petra","first_name":"Petra","last_name":"Rovó"},{"full_name":"Smith, Colin A.","first_name":"Colin A.","last_name":"Smith"},{"last_name":"Gauto","first_name":"Diego","full_name":"Gauto, Diego"},{"first_name":"Bert L.","last_name":"de Groot","full_name":"de Groot, Bert L."},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda"},{"last_name":"Linser","first_name":"Rasmus","full_name":"Linser, Rasmus"}],"volume":141,"date_updated":"2021-01-12T08:19:07Z","date_created":"2020-09-17T10:29:50Z","extern":"1","citation":{"mla":"Rovó, Petra, et al. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society, vol. 141, no. 2, American Chemical Society, 2019, pp. 858–69, doi:10.1021/jacs.8b09258.","short":"P. Rovó, C.A. Smith, D. Gauto, B.L. de Groot, P. Schanda, R. Linser, Journal of the American Chemical Society 141 (2019) 858–869.","chicago":"Rovó, Petra, Colin A. Smith, Diego Gauto, Bert L. de Groot, Paul Schanda, and Rasmus Linser. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.8b09258.","ama":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 2019;141(2):858-869. doi:10.1021/jacs.8b09258","ista":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. 2019. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 141(2), 858–869.","apa":"Rovó, P., Smith, C. A., Gauto, D., de Groot, B. L., Schanda, P., & Linser, R. (2019). Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09258","ieee":"P. Rovó, C. A. Smith, D. Gauto, B. L. de Groot, P. Schanda, and R. Linser, “Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques,” Journal of the American Chemical Society, vol. 141, no. 2. American Chemical Society, pp. 858–869, 2019."},"publication":"Journal of the American Chemical Society","page":"858-869","article_type":"original","date_published":"2019-01-08T00:00:00Z","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"article_processing_charge":"No","day":"08","_id":"8413","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 141","title":"Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques","status":"public","oa_version":"Submitted Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains."}]},{"status":"public","title":"Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR","intvolume":" 20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8412","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two‐state exchange process with a common exchange rate of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms, and an excited‐state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited‐state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid."}],"issue":"2","article_type":"original","page":"311-317","publication":"ChemPhysChem","citation":{"chicago":"Shannon, Matthew D., Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz, Witold K. Surewicz, Dominique Marion, Paul Schanda, and Christopher P. Jaroniec. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800779.","mla":"Shannon, Matthew D., et al. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 311–17, doi:10.1002/cphc.201800779.","short":"M.D. Shannon, T. Theint, D. Mukhopadhyay, K. Surewicz, W.K. Surewicz, D. Marion, P. Schanda, C.P. Jaroniec, ChemPhysChem 20 (2019) 311–317.","ista":"Shannon MD, Theint T, Mukhopadhyay D, Surewicz K, Surewicz WK, Marion D, Schanda P, Jaroniec CP. 2019. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 20(2), 311–317.","apa":"Shannon, M. D., Theint, T., Mukhopadhyay, D., Surewicz, K., Surewicz, W. K., Marion, D., … Jaroniec, C. P. (2019). Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800779","ieee":"M. D. Shannon et al., “Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 311–317, 2019.","ama":"Shannon MD, Theint T, Mukhopadhyay D, et al. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 2019;20(2):311-317. doi:10.1002/cphc.201800779"},"date_published":"2019-01-21T00:00:00Z","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"day":"21","article_processing_charge":"No","publication_status":"published","publisher":"Wiley","year":"2019","pmid":1,"date_updated":"2021-01-12T08:19:06Z","date_created":"2020-09-17T10:29:43Z","volume":20,"author":[{"full_name":"Shannon, Matthew D.","first_name":"Matthew D.","last_name":"Shannon"},{"full_name":"Theint, Theint","first_name":"Theint","last_name":"Theint"},{"last_name":"Mukhopadhyay","first_name":"Dwaipayan","full_name":"Mukhopadhyay, Dwaipayan"},{"first_name":"Krystyna","last_name":"Surewicz","full_name":"Surewicz, Krystyna"},{"first_name":"Witold K.","last_name":"Surewicz","full_name":"Surewicz, Witold K."},{"full_name":"Marion, Dominique","first_name":"Dominique","last_name":"Marion"},{"last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"},{"full_name":"Jaroniec, Christopher P.","first_name":"Christopher P.","last_name":"Jaroniec"}],"extern":"1","quality_controlled":"1","external_id":{"pmid":["30276945"]},"language":[{"iso":"eng"}],"doi":"10.1002/cphc.201800779","month":"01","publication_identifier":{"issn":["1439-4235"]}}]