[{"status":"public","article_type":"letter_note","type":"journal_article","_id":"8227","title":"AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody","author":[{"first_name":"Kristina M.","last_name":"Ilieva","full_name":"Ilieva, Kristina M."},{"last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit"},{"last_name":"Bax","full_name":"Bax, Heather J.","first_name":"Heather J."},{"first_name":"Silvia","last_name":"Crescioli","full_name":"Crescioli, Silvia"},{"last_name":"Montero‐Morales","full_name":"Montero‐Morales, Laura","first_name":"Laura"},{"last_name":"Mele","full_name":"Mele, Silvia","first_name":"Silvia"},{"first_name":"Heng Sheng","last_name":"Sow","full_name":"Sow, Heng Sheng"},{"first_name":"Chara","last_name":"Stavraka","full_name":"Stavraka, Chara"},{"last_name":"Josephs","full_name":"Josephs, Debra H.","first_name":"Debra H."},{"first_name":"James F.","last_name":"Spicer","full_name":"Spicer, James F."},{"first_name":"Herta","orcid":"0000-0003-4823-1505","full_name":"Steinkellner, Herta","last_name":"Steinkellner"},{"full_name":"Jensen‐Jarolim, Erika","orcid":"0000-0003-4019-5765","last_name":"Jensen‐Jarolim","first_name":"Erika"},{"full_name":"Tutt, Andrew N. J.","orcid":"0000-0001-8715-2901","last_name":"Tutt","first_name":"Andrew N. J."},{"first_name":"Sophia N.","full_name":"Karagiannis, Sophia N.","orcid":"0000-0002-4100-7810","last_name":"Karagiannis"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","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.","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.","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.","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."},"date_updated":"2021-01-12T08:17:35Z","month":"10","intvolume":" 74","quality_controlled":"1","publisher":"Wiley","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/all.13818"}],"oa":1,"oa_version":"Published Version","doi":"10.1111/all.13818","issue":"10","volume":74,"date_published":"2019-10-01T00:00:00Z","date_created":"2020-08-10T11:50:42Z","page":"1985-1989","day":"01","publication":"Allergy","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0105-4538","1398-9995"]},"year":"2019","publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"short":"P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary Biology 19 (2019).","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","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","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.","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.","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."},"date_updated":"2023-02-23T13:28:54Z","title":"Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow","article_processing_charge":"No","author":[{"full_name":"Shelyakin, Pavel V.","orcid":"0000-0003-0120-9319","last_name":"Shelyakin","first_name":"Pavel V."},{"first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639"},{"last_name":"Karan","full_name":"Karan, Anna A.","first_name":"Anna A."},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"article_number":"83","_id":"8263","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication":"BMC Evolutionary Biology","day":"27","year":"2019","publication_status":"published","publication_identifier":{"issn":["1471-2148"]},"date_created":"2020-08-15T11:04:07Z","volume":19,"date_published":"2019-03-27T00:00:00Z","doi":"10.1186/s12862-019-1403-6","oa_version":"Published Version","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."}],"intvolume":" 19","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12862-019-1403-6"}],"oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"month":"05","scopus_import":"1","quality_controlled":"1","publisher":"ACM","oa_version":"None","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."}],"doi":"10.1145/3317550.3321448","date_published":"2019-05-01T00:00:00Z","date_created":"2020-08-26T11:45:45Z","page":"105-112","day":"01","language":[{"iso":"eng"}],"publication":"Proceedings of the Workshop on Hot Topics in Operating Systems","publication_identifier":{"isbn":["9781450367271"]},"year":"2019","publication_status":"published","status":"public","type":"conference","conference":{"name":"HotOS: Workshop on Hot Topics in Operating Systems","end_date":"2019-05-15","location":"Bertinoro, Italy","start_date":"2019-05-13"},"_id":"8296","title":"Rethinking general-purpose decentralized computing","author":[{"first_name":"Enis Ceyhun","full_name":"Alp, Enis Ceyhun","last_name":"Alp"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"first_name":"Georgia","full_name":"Fragkouli, Georgia","last_name":"Fragkouli"},{"first_name":"Bryan","last_name":"Ford","full_name":"Ford, Bryan"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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.","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.","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.","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","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","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."},"date_updated":"2021-01-12T08:17:56Z"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","citation":{"ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. Cryptology ePrint Archive.","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. .","short":"A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, Cryptology EPrint Archive (n.d.).","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, 2019/1128.","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.","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."},"date_updated":"2021-09-24T12:08:14Z","title":"SoK: Communication across distributed ledgers","article_processing_charge":"No","author":[{"last_name":"Zamyatin","full_name":"Zamyatin, Alexei","first_name":"Alexei"},{"last_name":"Al-Bassam","full_name":"Al-Bassam, Mustafa","first_name":"Mustafa"},{"full_name":"Zindros, Dionysis","last_name":"Zindros","first_name":"Dionysis"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"first_name":"Pedro","last_name":"Moreno-Sanchez","full_name":"Moreno-Sanchez, Pedro"},{"first_name":"Aggelos","last_name":"Kiayias","full_name":"Kiayias, Aggelos"},{"last_name":"Knottenbelt","full_name":"Knottenbelt, William J.","first_name":"William J."}],"article_number":"2019/1128","_id":"8304","status":"public","type":"preprint","publication":"Cryptology ePrint Archive","language":[{"iso":"eng"}],"day":"01","publication_status":"submitted","year":"2019","date_created":"2020-08-26T12:16:38Z","date_published":"2019-10-01T00:00:00Z","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"10","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1128 "}],"oa":1},{"title":"Robust and scalable consensus for sharded distributed ledgers","article_processing_charge":"No","author":[{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","citation":{"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. .","short":"E. Kokoris Kogias, Cryptology EPrint Archive (n.d.).","ama":"Kokoris Kogias E. 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.","chicago":"Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, n.d.","ista":"Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive, 2019/676."},"date_updated":"2021-09-24T12:07:11Z","status":"public","type":"preprint","article_number":"2019/676","_id":"8303","date_created":"2020-08-26T12:13:56Z","date_published":"2019-06-06T00:00:00Z","publication":"Cryptology ePrint Archive","language":[{"iso":"eng"}],"day":"06","year":"2019","publication_status":"submitted","month":"06","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/676"}],"oa":1,"oa_version":"Preprint","abstract":[{"lang":"eng","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."}]}]