[{"doi":"10.48550/arXiv.1907.11183","arxiv":1,"type":"preprint","citation":{"ista":"Avvakumov S, Karasev R. Envy-free division using mapping degree. arXiv, 1907.11183.","short":"S. Avvakumov, R. Karasev, ArXiv (n.d.).","mla":"Avvakumov, Sergey, and Roman Karasev. “Envy-Free Division Using Mapping Degree.” <i>ArXiv</i>, 1907.11183, doi:<a href=\"https://doi.org/10.48550/arXiv.1907.11183\">10.48550/arXiv.1907.11183</a>.","chicago":"Avvakumov, Sergey, and Roman Karasev. “Envy-Free Division Using Mapping Degree.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1907.11183\">https://doi.org/10.48550/arXiv.1907.11183</a>.","ieee":"S. Avvakumov and R. Karasev, “Envy-free division using mapping degree,” <i>arXiv</i>. .","ama":"Avvakumov S, Karasev R. Envy-free division using mapping degree. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1907.11183\">10.48550/arXiv.1907.11183</a>","apa":"Avvakumov, S., &#38; Karasev, R. (n.d.). Envy-free division using mapping degree. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1907.11183\">https://doi.org/10.48550/arXiv.1907.11183</a>"},"article_processing_charge":"No","status":"public","_id":"8185","day":"25","related_material":{"link":[{"relation":"later_version","url":"https://doi.org/10.1112/mtk.12059"}],"record":[{"id":"8156","status":"public","relation":"dissertation_contains"}]},"date_updated":"2026-04-08T07:25:54Z","abstract":[{"text":"In this paper we study envy-free division problems. The classical approach to some of such problems, used by David Gale, reduces to considering continuous maps of a simplex to itself and finding sufficient conditions when this map hits the center of the simplex. The mere continuity is not sufficient for such a conclusion, the usual assumption (for example, in the Knaster--Kuratowski--Mazurkiewicz and the Gale theorem) is a certain boundary condition.\r\n  We follow Erel Segal-Halevi, Fr\\'ed\\'eric Meunier, and Shira Zerbib, and replace the boundary condition by another assumption, which has the economic meaning of possibility for a player to prefer an empty part in the segment\r\npartition problem. We solve the problem positively when $n$, the number of players that divide the segment, is a prime power, and we provide counterexamples for every $n$ which is not a prime power. We also provide counterexamples relevant to a wider class of fair or envy-free partition problems when $n$ is odd and not a prime power.","lang":"eng"}],"month":"07","oa_version":"Preprint","date_created":"2020-07-30T10:45:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Envy-free division using mapping degree","oa":1,"external_id":{"arxiv":["1907.11183"]},"language":[{"iso":"eng"}],"corr_author":"1","author":[{"orcid":"0000-0002-7840-5062","last_name":"Avvakumov","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey"},{"full_name":"Karasev, Roman","last_name":"Karasev","first_name":"Roman"}],"date_published":"2019-07-25T00:00:00Z","article_number":"1907.11183","project":[{"_id":"26611F5C-B435-11E9-9278-68D0E5697425","name":"Algorithms for Embeddings and Homotopy Theory","grant_number":"P31312","call_identifier":"FWF"}],"publication_status":"draft","department":[{"_id":"UlWa"}],"year":"2019","main_file_link":[{"url":"https://arxiv.org/abs/1907.11183","open_access":"1"}],"publication":"arXiv"},{"publication":"Allergy","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/all.13818"}],"quality_controlled":"1","page":"1985-1989","publication_status":"published","intvolume":"        74","year":"2019","author":[{"first_name":"Kristina M.","full_name":"Ilieva, Kristina M.","last_name":"Ilieva"},{"first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit","orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer"},{"last_name":"Bax","full_name":"Bax, Heather J.","first_name":"Heather J."},{"first_name":"Silvia","full_name":"Crescioli, Silvia","last_name":"Crescioli"},{"last_name":"Montero‐Morales","full_name":"Montero‐Morales, Laura","first_name":"Laura"},{"full_name":"Mele, Silvia","last_name":"Mele","first_name":"Silvia"},{"full_name":"Sow, Heng Sheng","last_name":"Sow","first_name":"Heng Sheng"},{"last_name":"Stavraka","full_name":"Stavraka, Chara","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."},{"first_name":"Herta","last_name":"Steinkellner","orcid":"0000-0003-4823-1505","full_name":"Steinkellner, Herta"},{"first_name":"Erika","full_name":"Jensen‐Jarolim, Erika","last_name":"Jensen‐Jarolim","orcid":"0000-0003-4019-5765"},{"first_name":"Andrew N. J.","last_name":"Tutt","orcid":"0000-0001-8715-2901","full_name":"Tutt, Andrew N. J."},{"first_name":"Sophia N.","full_name":"Karagiannis, Sophia N.","orcid":"0000-0002-4100-7810","last_name":"Karagiannis"}],"date_published":"2019-10-01T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"date_created":"2020-08-10T11:50:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody","oa_version":"Published Version","date_updated":"2021-01-12T08:17:35Z","issue":"10","month":"10","volume":74,"article_type":"letter_note","_id":"8227","day":"01","status":"public","citation":{"ama":"Ilieva KM, Singer J, Bax HJ, et al. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. <i>Allergy</i>. 2019;74(10):1985-1989. doi:<a href=\"https://doi.org/10.1111/all.13818\">10.1111/all.13818</a>","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. <i>Allergy</i>. Wiley. <a href=\"https://doi.org/10.1111/all.13818\">https://doi.org/10.1111/all.13818</a>","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.","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.","ieee":"K. M. Ilieva <i>et al.</i>, “AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody,” <i>Allergy</i>, vol. 74, no. 10. Wiley, pp. 1985–1989, 2019.","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.” <i>Allergy</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/all.13818\">https://doi.org/10.1111/all.13818</a>.","mla":"Ilieva, Kristina M., et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” <i>Allergy</i>, vol. 74, no. 10, Wiley, 2019, pp. 1985–89, doi:<a href=\"https://doi.org/10.1111/all.13818\">10.1111/all.13818</a>."},"publisher":"Wiley","article_processing_charge":"No","doi":"10.1111/all.13818","publication_identifier":{"issn":["0105-4538","1398-9995"]},"type":"journal_article"},{"doi":"10.1016/j.waojou.2019.100044","publisher":"Elsevier","day":"29","intvolume":"        12","year":"2019","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.waojou.2019.100044"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-10T11:50:54Z","oa":1,"language":[{"iso":"eng"}],"article_type":"original","abstract":[{"lang":"eng","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."}],"month":"07","volume":12,"date_updated":"2021-01-12T08:17:36Z","issue":"7","oa_version":"Published Version","type":"journal_article","publication_identifier":{"issn":["1939-4551"]},"article_processing_charge":"No","citation":{"apa":"Singer, J., Achatz-Straussberger, G., Bentley-Lukschal, A., Singer, J., Achatz, G., Karagiannis, S. N., &#38; Jensen-Jarolim, E. (2019). AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. <i>World Allergy Organization Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.waojou.2019.100044\">https://doi.org/10.1016/j.waojou.2019.100044</a>","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. <i>World Allergy Organization Journal</i>. 2019;12(7). doi:<a href=\"https://doi.org/10.1016/j.waojou.2019.100044\">10.1016/j.waojou.2019.100044</a>","mla":"Singer, Josef, et al. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” <i>World Allergy Organization Journal</i>, vol. 12, no. 7, 100044, Elsevier, 2019, doi:<a href=\"https://doi.org/10.1016/j.waojou.2019.100044\">10.1016/j.waojou.2019.100044</a>.","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.” <i>World Allergy Organization Journal</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.waojou.2019.100044\">https://doi.org/10.1016/j.waojou.2019.100044</a>.","ieee":"J. Singer <i>et al.</i>, “AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice,” <i>World Allergy Organization Journal</i>, vol. 12, no. 7. Elsevier, 2019.","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.","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)."},"_id":"8228","status":"public","publication_status":"published","quality_controlled":"1","publication":"World Allergy Organization Journal","extern":"1","title":"AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice","date_published":"2019-07-29T00:00:00Z","article_number":"100044","author":[{"last_name":"Singer","orcid":"0000-0002-8701-2412","full_name":"Singer, Josef","first_name":"Josef"},{"last_name":"Achatz-Straussberger","full_name":"Achatz-Straussberger, Gertrude","first_name":"Gertrude"},{"full_name":"Bentley-Lukschal, Anna","last_name":"Bentley-Lukschal","first_name":"Anna"},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit"},{"full_name":"Achatz, Gernot","last_name":"Achatz","first_name":"Gernot"},{"last_name":"Karagiannis","full_name":"Karagiannis, Sophia N.","first_name":"Sophia N."},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","first_name":"Erika"}]},{"publication_status":"published","quality_controlled":"1","publication":"Nutrients","extern":"1","title":"Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model","author":[{"full_name":"Ondracek, Anna S.","orcid":"0000-0001-7625-3651","last_name":"Ondracek","first_name":"Anna S."},{"last_name":"Heiden","full_name":"Heiden, Denise","first_name":"Denise"},{"last_name":"Oostingh","full_name":"Oostingh, Gertie J.","first_name":"Gertie J."},{"last_name":"Fuerst","full_name":"Fuerst, Elisabeth","first_name":"Elisabeth"},{"first_name":"Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas-Singer, Judit","orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer"},{"full_name":"Bergmayr, Cornelia","last_name":"Bergmayr","first_name":"Cornelia"},{"first_name":"Johanna","full_name":"Rohrhofer, Johanna","orcid":"0000-0002-2783-2099","last_name":"Rohrhofer"},{"orcid":"0000-0003-4019-5765","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","first_name":"Erika"},{"first_name":"Albert","orcid":"0000-0002-7034-9860","last_name":"Duschl","full_name":"Duschl, Albert"},{"full_name":"Untersmayr, Eva","orcid":"0000-0002-1963-499X","last_name":"Untersmayr","first_name":"Eva"}],"date_published":"2019-10-15T00:00:00Z","article_number":"2463","article_type":"original","date_updated":"2021-01-12T08:17:36Z","issue":"10","volume":11,"month":"10","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","publication_identifier":{"issn":["2072-6643"]},"type":"journal_article","citation":{"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).","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.","ieee":"A. S. Ondracek <i>et al.</i>, “Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model,” <i>Nutrients</i>, vol. 11, no. 10. MDPI, 2019.","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.” <i>Nutrients</i>. MDPI, 2019. <a href=\"https://doi.org/10.3390/nu11102463\">https://doi.org/10.3390/nu11102463</a>.","mla":"Ondracek, Anna S., et al. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” <i>Nutrients</i>, vol. 11, no. 10, 2463, MDPI, 2019, doi:<a href=\"https://doi.org/10.3390/nu11102463\">10.3390/nu11102463</a>.","ama":"Ondracek AS, Heiden D, Oostingh GJ, et al. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. <i>Nutrients</i>. 2019;11(10). doi:<a href=\"https://doi.org/10.3390/nu11102463\">10.3390/nu11102463</a>","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. <i>Nutrients</i>. MDPI. <a href=\"https://doi.org/10.3390/nu11102463\">https://doi.org/10.3390/nu11102463</a>"},"article_processing_charge":"No","_id":"8229","status":"public","year":"2019","intvolume":"        11","main_file_link":[{"url":"https://doi.org/10.3390/nu11102463","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-10T11:51:04Z","oa":1,"language":[{"iso":"eng"}],"doi":"10.3390/nu11102463","publisher":"MDPI","day":"15"},{"citation":{"short":"P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary Biology 19 (2019).","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,” <i>BMC Evolutionary Biology</i>, vol. 19. Springer Nature, 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.” <i>BMC Evolutionary Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1186/s12862-019-1403-6\">https://doi.org/10.1186/s12862-019-1403-6</a>.","mla":"Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” <i>BMC Evolutionary Biology</i>, vol. 19, 83, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1186/s12862-019-1403-6\">10.1186/s12862-019-1403-6</a>.","ama":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. <i>BMC Evolutionary Biology</i>. 2019;19. doi:<a href=\"https://doi.org/10.1186/s12862-019-1403-6\">10.1186/s12862-019-1403-6</a>","apa":"Shelyakin, P. V., Bochkareva, O., Karan, A. A., &#38; Gelfand, M. S. (2019). Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. <i>BMC Evolutionary Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12862-019-1403-6\">https://doi.org/10.1186/s12862-019-1403-6</a>"},"article_processing_charge":"No","publisher":"Springer Nature","publication_identifier":{"issn":["1471-2148"]},"doi":"10.1186/s12862-019-1403-6","type":"journal_article","_id":"8263","day":"27","status":"public","date_updated":"2023-02-23T13:28:54Z","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."}],"month":"03","volume":19,"article_type":"original","oa_version":"Published Version","oa":1,"date_created":"2020-08-15T11:04:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow","author":[{"last_name":"Shelyakin","orcid":"0000-0003-0120-9319","full_name":"Shelyakin, Pavel V.","first_name":"Pavel V."},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"last_name":"Karan","full_name":"Karan, Anna A.","first_name":"Anna A."},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"date_published":"2019-03-27T00:00:00Z","article_number":"83","language":[{"iso":"eng"}],"publication_status":"published","year":"2019","intvolume":"        19","publication":"BMC Evolutionary Biology","extern":"1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1186/s12862-019-1403-6","open_access":"1"}]},{"day":"06","_id":"8303","status":"public","type":"preprint","article_processing_charge":"No","citation":{"short":"E. Kokoris Kogias, Cryptology EPrint Archive (n.d.).","ista":"Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive, 2019/676.","chicago":"Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” <i>Cryptology EPrint Archive</i>, n.d.","ieee":"E. Kokoris Kogias, “Robust and scalable consensus for sharded distributed ledgers,” <i>Cryptology ePrint Archive</i>. .","mla":"Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” <i>Cryptology EPrint Archive</i>, 2019/676.","ama":"Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. <i>Cryptology ePrint Archive</i>.","apa":"Kokoris Kogias, E. (n.d.). Robust and scalable consensus for sharded distributed ledgers. <i>Cryptology ePrint Archive</i>."},"oa_version":"Preprint","month":"06","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"}],"date_updated":"2021-09-24T12:07:11Z","language":[{"iso":"eng"}],"date_published":"2019-06-06T00:00:00Z","article_number":"2019/676","author":[{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"}],"title":"Robust and scalable consensus for sharded distributed ledgers","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2020-08-26T12:13:56Z","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2019/676","open_access":"1"}],"extern":"1","publication":"Cryptology ePrint Archive","year":"2019","publication_status":"submitted"},{"supervisor":[{"first_name":"Bryan Alexander","last_name":"Ford","full_name":"Ford, Bryan Alexander"}],"_id":"8311","status":"public","day":"27","type":"dissertation","doi":"10.5075/epfl-thesis-7101","article_processing_charge":"No","publisher":"École Polytechnique Fédérale de Lausanne","citation":{"ista":"Kokoris Kogias E. 2019. Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne.","short":"E. Kokoris Kogias, Secure, Confidential Blockchains Providing High Throughput and Low Latency, École Polytechnique Fédérale de Lausanne, 2019.","mla":"Kokoris Kogias, Eleftherios. <i>Secure, Confidential Blockchains Providing High Throughput and Low Latency</i>. École Polytechnique Fédérale de Lausanne, 2019, doi:<a href=\"https://doi.org/10.5075/epfl-thesis-7101\">10.5075/epfl-thesis-7101</a>.","ieee":"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. <a href=\"https://doi.org/10.5075/epfl-thesis-7101\">https://doi.org/10.5075/epfl-thesis-7101</a>.","ama":"Kokoris Kogias E. Secure, confidential blockchains providing high throughput and low latency. 2019. doi:<a href=\"https://doi.org/10.5075/epfl-thesis-7101\">10.5075/epfl-thesis-7101</a>","apa":"Kokoris Kogias, E. (2019). <i>Secure, confidential blockchains providing high throughput and low latency</i>. École Polytechnique Fédérale de Lausanne. <a href=\"https://doi.org/10.5075/epfl-thesis-7101\">https://doi.org/10.5075/epfl-thesis-7101</a>"},"oa_version":"Published Version","month":"09","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."}],"date_updated":"2021-12-20T15:30:47Z","language":[{"iso":"eng"}],"date_published":"2019-09-27T00:00:00Z","author":[{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"}],"title":"Secure, confidential blockchains providing high throughput and low latency","date_created":"2020-08-27T11:22:24Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD","oa":1,"main_file_link":[{"url":"https://www.doi.org/10.5075/epfl-thesis-7101","open_access":"1"}],"extern":"1","year":"2019","page":"244","publication_status":"published"},{"article_processing_charge":"No","citation":{"mla":"Ford, Bryan, et al. <i>Methods and Systems for Secure Data Exchange</i>. 2019.","ieee":"B. Ford, L. Gasser, E. Kokoris Kogias, and P. Janovic, “Methods and systems for secure data exchange.” 2019.","chicago":"Ford, Bryan, Linus Gasser, Eleftherios Kokoris Kogias, and Philipp Janovic. “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.","short":"B. Ford, L. Gasser, E. Kokoris Kogias, P. Janovic, (2019).","apa":"Ford, B., Gasser, L., Kokoris Kogias, E., &#38; Janovic, P. (2019). Methods and systems for secure data exchange.","ama":"Ford B, Gasser L, Kokoris Kogias E, Janovic P. Methods and systems for secure data exchange. 2019."},"type":"patent","status":"public","_id":"8313","day":"22","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"}],"month":"08","date_updated":"2022-01-05T14:00:32Z","oa_version":"Published Version","oa":1,"title":"Methods and systems for secure data exchange","date_created":"2020-08-27T11:24:44Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2019-08-22T00:00:00Z","author":[{"full_name":"Ford, Bryan","last_name":"Ford","first_name":"Bryan"},{"first_name":"Linus","full_name":"Gasser, Linus","last_name":"Gasser"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Janovic, Philipp","last_name":"Janovic","first_name":"Philipp"}],"publication_date":"2019-08-22","year":"2019","applicant":["École Polytechnique Fédérale De Lausanne "],"ipn":"WO2019158209 (A1)","extern":"1","main_file_link":[{"open_access":"1","url":"https://patents.google.com/patent/WO2019158209A1"}],"ipc":"G06F21/62 ; H04L9/08 ; H04L9/32"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-27T11:36:54Z","title":"Brick: Asynchronous payment channels","oa":1,"external_id":{"arxiv":["1905.11360"]},"language":[{"iso":"eng"}],"author":[{"last_name":"Avarikioti","full_name":"Avarikioti, Georgia","first_name":"Georgia"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"first_name":"Roger","full_name":"Wattenhofer, Roger","last_name":"Wattenhofer"},{"last_name":"Zindros","full_name":"Zindros, Dionysis","first_name":"Dionysis"}],"date_published":"2019-05-27T00:00:00Z","article_number":"1905.11360","publication_status":"submitted","year":"2019","main_file_link":[{"url":"https://arxiv.org/abs/1905.11360","open_access":"1"}],"extern":"1","publication":"arXiv","doi":"10.48550/arXiv.1905.11360","arxiv":1,"type":"preprint","citation":{"ama":"Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1905.11360\">10.48550/arXiv.1905.11360</a>","apa":"Avarikioti, G., Kokoris Kogias, E., Wattenhofer, R., &#38; Zindros, D. (n.d.). Brick: Asynchronous payment channels. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1905.11360\">https://doi.org/10.48550/arXiv.1905.11360</a>","short":"G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, ArXiv (n.d.).","ista":"Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. arXiv, 1905.11360.","ieee":"G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous payment channels,” <i>arXiv</i>. .","chicago":"Avarikioti, Georgia, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Payment Channels.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1905.11360\">https://doi.org/10.48550/arXiv.1905.11360</a>.","mla":"Avarikioti, Georgia, et al. “Brick: Asynchronous Payment Channels.” <i>ArXiv</i>, 1905.11360, doi:<a href=\"https://doi.org/10.48550/arXiv.1905.11360\">10.48550/arXiv.1905.11360</a>."},"article_processing_charge":"No","_id":"8314","day":"27","status":"public","date_updated":"2025-06-26T11:26:45Z","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"}],"month":"05","oa_version":"Preprint"},{"year":"2019","publication_status":"submitted","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.10434"}],"extern":"1","publication":"arXiv","title":"Divide and scale: Formalization of distributed ledger sharding protocols","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-27T11:37:43Z","oa":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1910.10434"]},"article_number":"1910.10434","date_published":"2019-10-23T00:00:00Z","author":[{"first_name":"Georgia","last_name":"Avarikioti","full_name":"Avarikioti, Georgia"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Wattenhofer, Roger","last_name":"Wattenhofer","first_name":"Roger"}],"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"}],"month":"10","date_updated":"2025-06-26T11:28:33Z","oa_version":"Preprint","arxiv":1,"type":"preprint","doi":"10.48550/arXiv.1910.10434","article_processing_charge":"No","citation":{"ama":"Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1910.10434\">10.48550/arXiv.1910.10434</a>","apa":"Avarikioti, G., Kokoris Kogias, E., &#38; Wattenhofer, R. (n.d.). Divide and scale: Formalization of distributed ledger sharding protocols. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1910.10434\">https://doi.org/10.48550/arXiv.1910.10434</a>","ista":"Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. arXiv, 1910.10434.","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.” <i>ArXiv</i>, 1910.10434, doi:<a href=\"https://doi.org/10.48550/arXiv.1910.10434\">10.48550/arXiv.1910.10434</a>.","chicago":"Avarikioti, Georgia, Eleftherios Kokoris Kogias, and Roger Wattenhofer. “Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1910.10434\">https://doi.org/10.48550/arXiv.1910.10434</a>.","ieee":"G. Avarikioti, E. Kokoris Kogias, and R. Wattenhofer, “Divide and scale: Formalization of distributed ledger sharding protocols,” <i>arXiv</i>. ."},"status":"public","_id":"8315","day":"23"},{"intvolume":"        10","year":"2019","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-019-10490-9"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-17T10:28:25Z","oa":1,"external_id":{"pmid":["31217444"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41467-019-10490-9","publisher":"Springer Nature","day":"19","publication_status":"published","pmid":1,"quality_controlled":"1","extern":"1","publication":"Nature Communications","title":"Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex","author":[{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"first_name":"Leandro F.","last_name":"Estrozi","full_name":"Estrozi, Leandro F."},{"last_name":"Schwieters","full_name":"Schwieters, Charles D.","first_name":"Charles D."},{"first_name":"Gregory","last_name":"Effantin","full_name":"Effantin, Gregory"},{"first_name":"Pavel","last_name":"Macek","full_name":"Macek, Pavel"},{"first_name":"Remy","last_name":"Sounier","full_name":"Sounier, Remy"},{"first_name":"Astrid C.","full_name":"Sivertsen, Astrid C.","last_name":"Sivertsen"},{"full_name":"Schmidt, Elena","last_name":"Schmidt","first_name":"Elena"},{"first_name":"Rime","full_name":"Kerfah, Rime","last_name":"Kerfah"},{"first_name":"Guillaume","full_name":"Mas, Guillaume","last_name":"Mas"},{"last_name":"Colletier","full_name":"Colletier, Jacques-Philippe","first_name":"Jacques-Philippe"},{"first_name":"Peter","last_name":"Güntert","full_name":"Güntert, Peter"},{"last_name":"Favier","full_name":"Favier, Adrien","first_name":"Adrien"},{"first_name":"Guy","full_name":"Schoehn, Guy","last_name":"Schoehn"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"full_name":"Boisbouvier, Jerome","last_name":"Boisbouvier","first_name":"Jerome"}],"date_published":"2019-06-19T00:00:00Z","article_number":"2697","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"article_type":"original","date_updated":"2021-01-12T08:19:03Z","volume":10,"month":"06","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","publication_identifier":{"issn":["2041-1723"]},"type":"journal_article","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. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-10490-9\">https://doi.org/10.1038/s41467-019-10490-9</a>","ama":"Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-10490-9\">10.1038/s41467-019-10490-9</a>","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.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-10490-9\">https://doi.org/10.1038/s41467-019-10490-9</a>.","ieee":"D. F. Gauto <i>et al.</i>, “Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","mla":"Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” <i>Nature Communications</i>, vol. 10, 2697, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-10490-9\">10.1038/s41467-019-10490-9</a>.","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).","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."},"article_processing_charge":"No","_id":"8405","status":"public"},{"main_file_link":[{"open_access":"1","url":" https://doi.org/10.1126/sciadv.aaw3818"}],"intvolume":"         5","year":"2019","language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-17T10:28:36Z","day":"04","publisher":"American Association for the Advancement of Science","doi":"10.1126/sciadv.aaw3818","extern":"1","publication":"Science Advances","quality_controlled":"1","publication_status":"published","author":[{"full_name":"Felix, Jan","last_name":"Felix","first_name":"Jan"},{"full_name":"Weinhäupl, Katharina","last_name":"Weinhäupl","first_name":"Katharina"},{"last_name":"Chipot","full_name":"Chipot, Christophe","first_name":"Christophe"},{"full_name":"Dehez, François","last_name":"Dehez","first_name":"François"},{"first_name":"Audrey","full_name":"Hessel, Audrey","last_name":"Hessel"},{"last_name":"Gauto","full_name":"Gauto, Diego F.","first_name":"Diego F."},{"first_name":"Cecile","full_name":"Morlot, Cecile","last_name":"Morlot"},{"full_name":"Abian, Olga","last_name":"Abian","first_name":"Olga"},{"first_name":"Irina","last_name":"Gutsche","full_name":"Gutsche, Irina"},{"first_name":"Adrian","full_name":"Velazquez-Campoy, Adrian","last_name":"Velazquez-Campoy"},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"last_name":"Fraga","full_name":"Fraga, Hugo","first_name":"Hugo"}],"date_published":"2019-09-04T00:00:00Z","article_number":"eaaw3818","title":"Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors","oa_version":"Published Version","date_updated":"2021-01-12T08:19:03Z","issue":"9","abstract":[{"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.","lang":"eng"}],"volume":5,"month":"09","article_type":"original","_id":"8406","status":"public","citation":{"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. <i>Science Advances</i>. 2019;5(9). doi:<a href=\"https://doi.org/10.1126/sciadv.aaw3818\">10.1126/sciadv.aaw3818</a>","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. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.aaw3818\">https://doi.org/10.1126/sciadv.aaw3818</a>","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).","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.","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.” <i>Science Advances</i>. American Association for the Advancement of Science, 2019. <a href=\"https://doi.org/10.1126/sciadv.aaw3818\">https://doi.org/10.1126/sciadv.aaw3818</a>.","ieee":"J. Felix <i>et al.</i>, “Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors,” <i>Science Advances</i>, vol. 5, no. 9. American Association for the Advancement of Science, 2019.","mla":"Felix, Jan, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” <i>Science Advances</i>, vol. 5, no. 9, eaaw3818, American Association for the Advancement of Science, 2019, doi:<a href=\"https://doi.org/10.1126/sciadv.aaw3818\">10.1126/sciadv.aaw3818</a>."},"article_processing_charge":"No","publication_identifier":{"issn":["2375-2548"]},"type":"journal_article"},{"article_processing_charge":"No","citation":{"short":"P. Schanda, E.Y. Chekmenev, ChemPhysChem 20 (2019) 177–177.","ista":"Schanda P, Chekmenev EY. 2019. NMR for Biological Systems. ChemPhysChem. 20(2), 177–177.","ieee":"P. Schanda and E. Y. Chekmenev, “NMR for Biological Systems,” <i>ChemPhysChem</i>, vol. 20, no. 2. Wiley, pp. 177–177, 2019.","chicago":"Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” <i>ChemPhysChem</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cphc.201801100\">https://doi.org/10.1002/cphc.201801100</a>.","mla":"Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” <i>ChemPhysChem</i>, vol. 20, no. 2, Wiley, 2019, pp. 177–177, doi:<a href=\"https://doi.org/10.1002/cphc.201801100\">10.1002/cphc.201801100</a>.","ama":"Schanda P, Chekmenev EY. NMR for Biological Systems. <i>ChemPhysChem</i>. 2019;20(2):177-177. doi:<a href=\"https://doi.org/10.1002/cphc.201801100\">10.1002/cphc.201801100</a>","apa":"Schanda, P., &#38; Chekmenev, E. Y. (2019). NMR for Biological Systems. <i>ChemPhysChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cphc.201801100\">https://doi.org/10.1002/cphc.201801100</a>"},"type":"journal_article","publication_identifier":{"issn":["1439-4235"]},"status":"public","_id":"8410","volume":20,"month":"01","issue":"2","date_updated":"2021-01-12T08:19:05Z","article_type":"letter_note","oa_version":"Published Version","title":"NMR for Biological Systems","date_published":"2019-01-21T00:00:00Z","author":[{"last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"full_name":"Chekmenev, Eduard Y.","last_name":"Chekmenev","first_name":"Eduard Y."}],"publication_status":"published","page":"177-177","publication":"ChemPhysChem","extern":"1","quality_controlled":"1","pmid":1,"publisher":"Wiley","doi":"10.1002/cphc.201801100","day":"21","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-17T10:29:26Z","language":[{"iso":"eng"}],"external_id":{"pmid":["30556633"]},"year":"2019","intvolume":"        20","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/cphc.201801100"}]},{"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-17T10:41:27Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["1809.08947"]},"intvolume":"       374","year":"2019","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.08947"}],"publisher":"Springer Nature","arxiv":1,"doi":"10.1007/s00220-019-03448-x","day":"09","title":"Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards","date_published":"2019-05-09T00:00:00Z","author":[{"first_name":"Péter","full_name":"Bálint, Péter","last_name":"Bálint"},{"full_name":"De Simoi, Jacopo","last_name":"De Simoi","first_name":"Jacopo"},{"first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"},{"first_name":"Martin","full_name":"Leguil, Martin","last_name":"Leguil"}],"publication_status":"published","page":"1531-1575","extern":"1","publication":"Communications in Mathematical Physics","quality_controlled":"1","article_processing_charge":"No","citation":{"ama":"Bálint P, De Simoi J, Kaloshin V, Leguil M. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. <i>Communications in Mathematical Physics</i>. 2019;374(3):1531-1575. doi:<a href=\"https://doi.org/10.1007/s00220-019-03448-x\">10.1007/s00220-019-03448-x</a>","apa":"Bálint, P., De Simoi, J., Kaloshin, V., &#38; Leguil, M. (2019). Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-019-03448-x\">https://doi.org/10.1007/s00220-019-03448-x</a>","ista":"Bálint P, De Simoi J, Kaloshin V, Leguil M. 2019. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 374(3), 1531–1575.","short":"P. Bálint, J. De Simoi, V. Kaloshin, M. Leguil, Communications in Mathematical Physics 374 (2019) 1531–1575.","mla":"Bálint, Péter, et al. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” <i>Communications in Mathematical Physics</i>, vol. 374, no. 3, Springer Nature, 2019, pp. 1531–75, doi:<a href=\"https://doi.org/10.1007/s00220-019-03448-x\">10.1007/s00220-019-03448-x</a>.","ieee":"P. Bálint, J. De Simoi, V. Kaloshin, and M. Leguil, “Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards,” <i>Communications in Mathematical Physics</i>, vol. 374, no. 3. Springer Nature, pp. 1531–1575, 2019.","chicago":"Bálint, Péter, Jacopo De Simoi, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00220-019-03448-x\">https://doi.org/10.1007/s00220-019-03448-x</a>."},"type":"journal_article","publication_identifier":{"issn":["0010-3616","1432-0916"]},"status":"public","_id":"8415","month":"05","abstract":[{"lang":"eng","text":"We consider billiards obtained by removing three strictly convex obstacles satisfying the non-eclipse condition on the plane. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift on three symbols that provides a natural labeling of all periodic orbits. We study the following inverse problem: does the Marked Length Spectrum (i.e., the set of lengths of periodic orbits together with their labeling), determine the geometry of the billiard table? We show that from the Marked Length Spectrum it is possible to recover the curvature at periodic points of period two, as well as the Lyapunov exponent of each periodic orbit."}],"volume":374,"issue":"3","date_updated":"2021-01-12T08:19:08Z","article_type":"original","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"oa_version":"Preprint"},{"article_type":"original","volume":19,"month":"04","abstract":[{"text":"In this paper, we show that any smooth one-parameter deformations of a strictly convex integrable billiard table Ω0 preserving the integrability near the boundary have to be tangent to a finite dimensional space passing through Ω0.","lang":"eng"}],"date_updated":"2021-01-12T08:19:08Z","issue":"2","oa_version":"Preprint","type":"journal_article","publication_identifier":{"issn":["1609-4514"]},"article_processing_charge":"No","citation":{"apa":"Huang, G., &#38; Kaloshin, V. (2019). On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. <i>Moscow Mathematical Journal</i>. American Mathematical Society. <a href=\"https://doi.org/10.17323/1609-4514-2019-19-2-307-327\">https://doi.org/10.17323/1609-4514-2019-19-2-307-327</a>","ama":"Huang G, Kaloshin V. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. <i>Moscow Mathematical Journal</i>. 2019;19(2):307-327. doi:<a href=\"https://doi.org/10.17323/1609-4514-2019-19-2-307-327\">10.17323/1609-4514-2019-19-2-307-327</a>","chicago":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” <i>Moscow Mathematical Journal</i>. American Mathematical Society, 2019. <a href=\"https://doi.org/10.17323/1609-4514-2019-19-2-307-327\">https://doi.org/10.17323/1609-4514-2019-19-2-307-327</a>.","ieee":"G. Huang and V. Kaloshin, “On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables,” <i>Moscow Mathematical Journal</i>, vol. 19, no. 2. American Mathematical Society, pp. 307–327, 2019.","mla":"Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” <i>Moscow Mathematical Journal</i>, vol. 19, no. 2, American Mathematical Society, 2019, pp. 307–27, doi:<a href=\"https://doi.org/10.17323/1609-4514-2019-19-2-307-327\">10.17323/1609-4514-2019-19-2-307-327</a>.","short":"G. Huang, V. Kaloshin, Moscow Mathematical Journal 19 (2019) 307–327.","ista":"Huang G, Kaloshin V. 2019. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. 19(2), 307–327."},"status":"public","_id":"8416","page":"307-327","publication_status":"published","quality_controlled":"1","publication":"Moscow Mathematical Journal","extern":"1","title":"On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables","date_published":"2019-04-01T00:00:00Z","author":[{"first_name":"Guan","full_name":"Huang, Guan","last_name":"Huang"},{"full_name":"Kaloshin, Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"arxiv":1,"doi":"10.17323/1609-4514-2019-19-2-307-327","publisher":"American Mathematical Society","day":"01","intvolume":"        19","year":"2019","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.09341"}],"date_created":"2020-09-17T10:41:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1809.09341"]}},{"publisher":"Springer Nature","doi":"10.1007/s00205-019-01368-7","day":"12","oa":1,"date_created":"2020-09-17T10:41:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"intvolume":"       233","year":"2019","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00205-019-01368-7"}],"citation":{"chicago":"Guardia, Marcel, Vadim Kaloshin, and Jianlu Zhang. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00205-019-01368-7\">https://doi.org/10.1007/s00205-019-01368-7</a>.","ieee":"M. Guardia, V. Kaloshin, and J. Zhang, “Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 233, no. 2. Springer Nature, pp. 799–836, 2019.","mla":"Guardia, Marcel, et al. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 233, no. 2, Springer Nature, 2019, pp. 799–836, doi:<a href=\"https://doi.org/10.1007/s00205-019-01368-7\">10.1007/s00205-019-01368-7</a>.","short":"M. Guardia, V. Kaloshin, J. Zhang, Archive for Rational Mechanics and Analysis 233 (2019) 799–836.","ista":"Guardia M, Kaloshin V, Zhang J. 2019. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. 233(2), 799–836.","apa":"Guardia, M., Kaloshin, V., &#38; Zhang, J. (2019). Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-019-01368-7\">https://doi.org/10.1007/s00205-019-01368-7</a>","ama":"Guardia M, Kaloshin V, Zhang J. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. <i>Archive for Rational Mechanics and Analysis</i>. 2019;233(2):799-836. doi:<a href=\"https://doi.org/10.1007/s00205-019-01368-7\">10.1007/s00205-019-01368-7</a>"},"article_processing_charge":"No","publication_identifier":{"issn":["0003-9527","1432-0673"]},"type":"journal_article","status":"public","_id":"8418","date_updated":"2021-01-12T08:19:09Z","issue":"2","abstract":[{"lang":"eng","text":"For the Restricted Circular Planar 3 Body Problem, we show that there exists an open set U in phase space of fixed measure, where the set of initial points which lead to collision is O(μ120) dense as μ→0."}],"volume":233,"month":"03","article_type":"original","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"oa_version":"Published Version","title":"Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem","author":[{"first_name":"Marcel","full_name":"Guardia, Marcel","last_name":"Guardia"},{"full_name":"Kaloshin, Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"first_name":"Jianlu","full_name":"Zhang, Jianlu","last_name":"Zhang"}],"date_published":"2019-03-12T00:00:00Z","page":"799-836","publication_status":"published","publication":"Archive for Rational Mechanics and Analysis","extern":"1","quality_controlled":"1"},{"conference":{"start_date":"2019-04-15","location":"Montreal, Canada","end_date":"2019-04-15","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems"},"title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics","author":[{"first_name":"Matthias","last_name":"Althoff","full_name":"Althoff, Matthias"},{"first_name":"Stanley","full_name":"Bak, Stanley","last_name":"Bak"},{"last_name":"Forets","full_name":"Forets, Marcelo","first_name":"Marcelo"},{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"first_name":"Niklas","last_name":"Kochdumper","full_name":"Kochdumper, Niklas"},{"first_name":"Rajarshi","full_name":"Ray, Rajarshi","last_name":"Ray"},{"full_name":"Schilling, Christian","last_name":"Schilling","orcid":"0000-0003-3658-1065","first_name":"Christian","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schupp, Stefan","last_name":"Schupp","first_name":"Stefan"}],"date_published":"2019-05-25T00:00:00Z","publication_status":"published","page":"14-40","publication":"EPiC Series in Computing","quality_controlled":"1","citation":{"ama":"Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In: <i>EPiC Series in Computing</i>. Vol 61. EasyChair; 2019:14-40. doi:<a href=\"https://doi.org/10.29007/bj1w\">10.29007/bj1w</a>","apa":"Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp, S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In <i>EPiC Series in Computing</i> (Vol. 61, pp. 14–40). Montreal, Canada: EasyChair. <a href=\"https://doi.org/10.29007/bj1w\">https://doi.org/10.29007/bj1w</a>","short":"M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling, S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40.","ista":"Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40.","chicago":"Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper, Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” In <i>EPiC Series in Computing</i>, 61:14–40. EasyChair, 2019. <a href=\"https://doi.org/10.29007/bj1w\">https://doi.org/10.29007/bj1w</a>.","ieee":"M. Althoff <i>et al.</i>, “ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics,” in <i>EPiC Series in Computing</i>, Montreal, Canada, 2019, vol. 61, pp. 14–40.","mla":"Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” <i>EPiC Series in Computing</i>, vol. 61, EasyChair, 2019, pp. 14–40, doi:<a href=\"https://doi.org/10.29007/bj1w\">10.29007/bj1w</a>."},"article_processing_charge":"No","publication_identifier":{"eissn":["2398-7340"]},"type":"conference","status":"public","_id":"8570","date_updated":"2026-06-18T19:33:41Z","abstract":[{"text":"This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.</jats:p>","lang":"eng"}],"month":"05","volume":61,"oa_version":"Published Version","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-26T14:23:54Z","corr_author":"1","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"intvolume":"        61","year":"2019","main_file_link":[{"url":"https://easychair.org/publications/open/1gbP","open_access":"1"}],"publisher":"EasyChair","doi":"10.29007/bj1w","day":"25","scopus_import":"1","ddc":["000"]},{"language":[{"iso":"eng"}],"external_id":{"arxiv":["1908.02523"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-10-21T15:25:45Z","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1908.02523"}],"intvolume":"        24","year":"2019","day":"10","arxiv":1,"doi":"10.1134/S1560354719060017","publisher":"Springer","date_published":"2019-12-10T00:00:00Z","author":[{"full_name":"Chierchia, Luigi","last_name":"Chierchia","first_name":"Luigi"},{"orcid":"0000-0003-2640-4049","last_name":"Koudjinan","full_name":"Koudjinan, Edmond","id":"52DF3E68-AEFA-11EA-95A4-124A3DDC885E","first_name":"Edmond"}],"title":"V. I. Arnold’s “pointwise” KAM theorem","quality_controlled":"1","publication":"Regular and Chaotic Dynamics","extern":"1","publication_status":"published","page":"583–606","_id":"8693","status":"public","type":"journal_article","article_processing_charge":"No","citation":{"apa":"Chierchia, L., &#38; Koudjinan, E. (2019). V. I. Arnold’s “pointwise” KAM theorem. <i>Regular and Chaotic Dynamics</i>. Springer. <a href=\"https://doi.org/10.1134/S1560354719060017\">https://doi.org/10.1134/S1560354719060017</a>","ama":"Chierchia L, Koudjinan E. V. I. Arnold’s “pointwise” KAM theorem. <i>Regular and Chaotic Dynamics</i>. 2019;24:583–606. doi:<a href=\"https://doi.org/10.1134/S1560354719060017\">10.1134/S1560354719060017</a>","mla":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” <i>Regular and Chaotic Dynamics</i>, vol. 24, Springer, 2019, pp. 583–606, doi:<a href=\"https://doi.org/10.1134/S1560354719060017\">10.1134/S1560354719060017</a>.","ieee":"L. Chierchia and E. Koudjinan, “V. I. Arnold’s ‘pointwise’ KAM theorem,” <i>Regular and Chaotic Dynamics</i>, vol. 24. Springer, pp. 583–606, 2019.","chicago":"Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” <i>Regular and Chaotic Dynamics</i>. Springer, 2019. <a href=\"https://doi.org/10.1134/S1560354719060017\">https://doi.org/10.1134/S1560354719060017</a>.","ista":"Chierchia L, Koudjinan E. 2019. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 24, 583–606.","short":"L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 24 (2019) 583–606."},"oa_version":"Preprint","article_type":"original","abstract":[{"lang":"eng","text":"We review V. I. Arnold’s 1963 celebrated paper [1] Proof of A. N. Kolmogorov’s Theorem on the Conservation of Conditionally Periodic Motions with a Small Variation in the Hamiltonian, and prove that, optimising Arnold’s scheme, one can get “sharp” asymptotic quantitative conditions (as ε → 0, ε being the strength of the perturbation). All constants involved are explicitly computed."}],"volume":24,"month":"12","date_updated":"2021-01-12T08:20:34Z"},{"oa":1,"date_created":"2021-01-19T10:59:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"year":"2019","intvolume":"        20","main_file_link":[{"url":" https://doi.org/10.1002/cbic.201800633","open_access":"1"}],"publisher":"Wiley","doi":"10.1002/cbic.201800633","day":"01","title":"Recognition of ASF1 by using hydrocarbon‐constrained peptides","date_published":"2019-04-01T00:00:00Z","author":[{"full_name":"Bakail, May M","orcid":"0000-0002-9592-1587","last_name":"Bakail","first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E"},{"last_name":"Rodriguez‐Marin","full_name":"Rodriguez‐Marin, Silvia","first_name":"Silvia"},{"first_name":"Zsófia","full_name":"Hegedüs, Zsófia","last_name":"Hegedüs"},{"first_name":"Marie E.","full_name":"Perrin, Marie E.","last_name":"Perrin"},{"full_name":"Ochsenbein, Françoise","last_name":"Ochsenbein","first_name":"Françoise"},{"last_name":"Wilson","full_name":"Wilson, Andrew J.","first_name":"Andrew J."}],"page":"891-895","publication_status":"published","extern":"1","publication":"ChemBioChem","quality_controlled":"1","article_processing_charge":"No","citation":{"ama":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by using hydrocarbon‐constrained peptides. <i>ChemBioChem</i>. 2019;20(7):891-895. doi:<a href=\"https://doi.org/10.1002/cbic.201800633\">10.1002/cbic.201800633</a>","apa":"Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein, F., &#38; Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained peptides. <i>ChemBioChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cbic.201800633\">https://doi.org/10.1002/cbic.201800633</a>","short":"M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein, A.J. Wilson, ChemBioChem 20 (2019) 891–895.","ista":"Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. 2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 20(7), 891–895.","chicago":"Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin, Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” <i>ChemBioChem</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/cbic.201800633\">https://doi.org/10.1002/cbic.201800633</a>.","ieee":"M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein, and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,” <i>ChemBioChem</i>, vol. 20, no. 7. Wiley, pp. 891–895, 2019.","mla":"Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” <i>ChemBioChem</i>, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:<a href=\"https://doi.org/10.1002/cbic.201800633\">10.1002/cbic.201800633</a>."},"type":"journal_article","publication_identifier":{"issn":["1439-4227","1439-7633"]},"_id":"9016","status":"public","volume":20,"month":"04","abstract":[{"lang":"eng","text":"Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118–135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation occurs."}],"date_updated":"2023-02-23T13:46:48Z","issue":"7","article_type":"original","oa_version":"Published Version"},{"status":"public","_id":"9018","publication_identifier":{"issn":["2451-9456"]},"type":"journal_article","citation":{"apa":"Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E., … Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. <i>Cell Chemical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">https://doi.org/10.1016/j.chembiol.2019.09.002</a>","ama":"Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. <i>Cell Chemical Biology</i>. 2019;26(11):1573-1585.e10. doi:<a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">10.1016/j.chembiol.2019.09.002</a>","ieee":"M. M. Bakail <i>et al.</i>, “Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1,” <i>Cell Chemical Biology</i>, vol. 26, no. 11. Elsevier, p. 1573–1585.e10, 2019.","chicago":"Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” <i>Cell Chemical Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">https://doi.org/10.1016/j.chembiol.2019.09.002</a>.","mla":"Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” <i>Cell Chemical Biology</i>, vol. 26, no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:<a href=\"https://doi.org/10.1016/j.chembiol.2019.09.002\">10.1016/j.chembiol.2019.09.002</a>.","short":"M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C. Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N. Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin, G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26 (2019) 1573–1585.e10.","ista":"Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C, Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11), 1573–1585.e10."},"article_processing_charge":"No","oa_version":"Published Version","article_type":"original","keyword":["Clinical Biochemistry","Molecular Medicine","Biochemistry","Molecular Biology","Pharmacology","Drug Discovery"],"date_updated":"2023-02-23T13:46:53Z","issue":"11","abstract":[{"lang":"eng","text":"Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy."}],"volume":26,"month":"11","author":[{"orcid":"0000-0002-9592-1587","last_name":"Bakail","full_name":"Bakail, May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","first_name":"May M"},{"first_name":"Albane","last_name":"Gaubert","full_name":"Gaubert, Albane"},{"first_name":"Jessica","full_name":"Andreani, Jessica","last_name":"Andreani"},{"full_name":"Moal, Gwenaëlle","last_name":"Moal","first_name":"Gwenaëlle"},{"last_name":"Pinna","full_name":"Pinna, Guillaume","first_name":"Guillaume"},{"last_name":"Boyarchuk","full_name":"Boyarchuk, Ekaterina","first_name":"Ekaterina"},{"first_name":"Marie-Cécile","last_name":"Gaillard","full_name":"Gaillard, Marie-Cécile"},{"first_name":"Regis","full_name":"Courbeyrette, Regis","last_name":"Courbeyrette"},{"first_name":"Carl","last_name":"Mann","full_name":"Mann, Carl"},{"full_name":"Thuret, Jean-Yves","last_name":"Thuret","first_name":"Jean-Yves"},{"full_name":"Guichard, Bérengère","last_name":"Guichard","first_name":"Bérengère"},{"full_name":"Murciano, Brice","last_name":"Murciano","first_name":"Brice"},{"last_name":"Richet","full_name":"Richet, Nicolas","first_name":"Nicolas"},{"first_name":"Adeline","full_name":"Poitou, Adeline","last_name":"Poitou"},{"last_name":"Frederic","full_name":"Frederic, Claire","first_name":"Claire"},{"last_name":"Le Du","full_name":"Le Du, Marie-Hélène","first_name":"Marie-Hélène"},{"last_name":"Agez","full_name":"Agez, Morgane","first_name":"Morgane"},{"full_name":"Roelants, Caroline","last_name":"Roelants","first_name":"Caroline"},{"last_name":"Gurard-Levin","full_name":"Gurard-Levin, Zachary A.","first_name":"Zachary A."},{"last_name":"Almouzni","full_name":"Almouzni, Geneviève","first_name":"Geneviève"},{"last_name":"Cherradi","full_name":"Cherradi, Nadia","first_name":"Nadia"},{"full_name":"Guerois, Raphael","last_name":"Guerois","first_name":"Raphael"},{"first_name":"Françoise","last_name":"Ochsenbein","full_name":"Ochsenbein, Françoise"}],"date_published":"2019-11-21T00:00:00Z","title":"Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1","pmid":1,"quality_controlled":"1","publication":"Cell Chemical Biology","extern":"1","publication_status":"published","page":"1573-1585.e10","day":"21","doi":"10.1016/j.chembiol.2019.09.002","publisher":"Elsevier","external_id":{"pmid":["31543461"]},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-01-19T11:04:50Z","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.chembiol.2019.09.002","open_access":"1"}],"year":"2019","intvolume":"        26"}]