[{"doi":"10.1038/s41431-021-00836-7","author":[{"first_name":"Sergei A.","last_name":"Slavskii","full_name":"Slavskii, Sergei A."},{"first_name":"Ivan A.","last_name":"Kuznetsov","full_name":"Kuznetsov, Ivan A."},{"full_name":"Shashkova, Tatiana I.","first_name":"Tatiana I.","last_name":"Shashkova"},{"full_name":"Bazykin, Georgii A.","last_name":"Bazykin","first_name":"Georgii A."},{"full_name":"Axenovich, Tatiana I.","last_name":"Axenovich","first_name":"Tatiana I."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor"},{"last_name":"Aulchenko","first_name":"Yurii S.","full_name":"Aulchenko, Yurii S."}],"date_created":"2021-08-15T22:01:28Z","_id":"9910","scopus_import":"1","oa":1,"date_published":"2021-07-01T00:00:00Z","citation":{"mla":"Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>, vol. 29, no. 7, Springer Nature, 2021, pp. 1082–91, doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>.","chicago":"Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The Limits of Normal Approximation for Adult Height.” <i>European Journal of Human Genetics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>.","short":"S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich, F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.","ama":"Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. 2021;29(7):1082-1091. doi:<a href=\"https://doi.org/10.1038/s41431-021-00836-7\">10.1038/s41431-021-00836-7</a>","apa":"Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., &#38; Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. <i>European Journal of Human Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41431-021-00836-7\">https://doi.org/10.1038/s41431-021-00836-7</a>","ista":"Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European Journal of Human Genetics. 29(7), 1082–1091.","ieee":"S. A. Slavskii <i>et al.</i>, “The limits of normal approximation for adult height,” <i>European Journal of Human Genetics</i>, vol. 29, no. 7. Springer Nature, pp. 1082–1091, 2021."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        29","acknowledgement":"We are grateful to Marianna Bevova and Pavel Borodin for fruitful discussion and help with conceptualising our findings and to Lennart C. Karssen for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects in control of complex human traits”). The work of SAS, IAK, and TIS were supported by Russian Ministry of Science and Education under the 5–100 Excellence Programme. The work of YSA and TIA was supported by the Ministry of Education and Science of the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4). FAK is supported by the ERC Consolidator Grant (ChrFL: 771209).","publication_identifier":{"eissn":["1476-5438"],"issn":["1018-4813"]},"volume":29,"article_type":"original","page":"1082-1091","quality_controlled":"1","file_date_updated":"2021-08-16T09:14:36Z","abstract":[{"text":"Adult height inspired the first biometrical and quantitative genetic studies and is a test-case trait for understanding heritability. The studies of height led to formulation of the classical polygenic model, that has a profound influence on the way we view and analyse complex traits. An essential part of the classical model is an assumption of additivity of effects and normality of the distribution of the residuals. However, it may be expected that the normal approximation will become insufficient in bigger studies. Here, we demonstrate that when the height of hundreds of thousands of individuals is analysed, the model complexity needs to be increased to include non-additive interactions between sex, environment and genes. Alternatively, the use of log-normal approximation allowed us to still use the additive effects model. These findings are important for future genetic and methodologic studies that make use of adult height as an exemplar trait.","lang":"eng"}],"pmid":1,"publication_status":"published","title":"The limits of normal approximation for adult height","oa_version":"Published Version","publisher":"Springer Nature","month":"07","issue":"7","day":"01","ec_funded":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"type":"journal_article","project":[{"grant_number":"771209","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"year":"2021","external_id":{"pmid":["33664501"],"isi":["000625853200001"]},"status":"public","article_processing_charge":"Yes (in subscription journal)","publication":"European Journal of Human Genetics","department":[{"_id":"FyKo"}],"isi":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"file":[{"date_updated":"2021-08-16T09:14:36Z","file_size":1079395,"content_type":"application/pdf","success":1,"relation":"main_file","date_created":"2021-08-16T09:14:36Z","checksum":"a676d76f91b0dbe0504c63e469129c2a","file_id":"9921","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","creator":"asandaue","access_level":"open_access"}],"date_updated":"2025-07-10T12:02:05Z","ddc":["576"]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1,"year":"2021","project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","grant_number":"771209"}],"type":"journal_article","month":"07","publisher":"Springer Nature","day":"30","issue":"1","related_material":{"link":[{"description":"News on IST Website","url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"20811"}]},"language":[{"iso":"eng"}],"ddc":["570","610"],"date_updated":"2026-04-07T12:34:57Z","file":[{"relation":"main_file","creator":"asandaue","access_level":"open_access","date_created":"2021-08-16T11:36:49Z","checksum":"ac86892ed17e6724c7251844da5cef5c","file_id":"9927","file_name":"2021_ScientificReports_Rella.pdf","success":1,"date_updated":"2021-08-16T11:36:49Z","file_size":3432001,"content_type":"application/pdf"}],"status":"public","external_id":{"isi":["000683329100001"],"pmid":["34330988"]},"article_number":"15729","publication":"Scientific Reports","department":[{"_id":"FyKo"}],"has_accepted_license":"1","isi":1,"article_processing_charge":"Yes","intvolume":"        11","acknowledgement":"We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta, Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España for useful comments. The opinions expressed in this document are exclusively of the authors and, therefore, do not necessarily coincide with those of the Banco de España or the Eurosystem. ETD is supported by the Swiss National Science and Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator Grant (771209-CharFL).","publication_identifier":{"eissn":["2045-2322"]},"volume":11,"article_type":"original","_id":"9905","scopus_import":"1","date_created":"2021-08-15T22:01:26Z","doi":"10.1038/s41598-021-95025-3","author":[{"id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","full_name":"Rella, Simon","last_name":"Rella","first_name":"Simon"},{"full_name":"Kulikova, Yuliya A.","first_name":"Yuliya A.","last_name":"Kulikova"},{"last_name":"Dermitzakis","first_name":"Emmanouil T.","full_name":"Dermitzakis, Emmanouil T."},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-07-30T00:00:00Z","oa":1,"citation":{"ieee":"S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,” <i>Scientific Reports</i>, vol. 11, no. 1. Springer Nature, 2021.","ista":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 11(1), 15729.","apa":"Rella, S., Kulikova, Y. A., Dermitzakis, E. T., &#38; Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>","chicago":"Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41598-021-95025-3\">https://doi.org/10.1038/s41598-021-95025-3</a>.","mla":"Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.” <i>Scientific Reports</i>, vol. 11, no. 1, 15729, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>.","short":"S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports 11 (2021).","ama":"Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. <i>Scientific Reports</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.1038/s41598-021-95025-3\">10.1038/s41598-021-95025-3</a>"},"abstract":[{"lang":"eng","text":"Vaccines are thought to be the best available solution for controlling the ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains may come too rapidly for current vaccine developments to alleviate the health, economic and social consequences of the pandemic. To quantify and characterize the risk of such a scenario, we created a SIR-derived model with initial stochastic dynamics of the vaccine-resistant strain to study the probability of its emergence and establishment. Using parameters realistically resembling SARS-CoV-2 transmission, we model a wave-like pattern of the pandemic and consider the impact of the rate of vaccination and the strength of non-pharmaceutical intervention measures on the probability of emergence of a resistant strain. As expected, we found that a fast rate of vaccination decreases the probability of emergence of a resistant strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions happened at a time when most individuals of the population have already been vaccinated the probability of emergence of a resistant strain was greatly increased. Consequently, we show that a period of transmission reduction close to the end of the vaccination campaign can substantially reduce the probability of resistant strain establishment. Our results suggest that policymakers and individuals should consider maintaining non-pharmaceutical interventions and transmission-reducing behaviours throughout the entire vaccination period."}],"pmid":1,"title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","oa_version":"Published Version","publication_status":"published","quality_controlled":"1","file_date_updated":"2021-08-16T11:36:49Z"},{"abstract":[{"text":"A mesophilic methanogenic culture, designated JL01, was isolated from Holocene permafrost in the Russian Arctic [1]. After long-term extensive cultivation at 15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial (Sphaerochaeta associata GLS2) strains.\r\nStrain JL01 was a strict anaerobe and grew on methanol, acetate and methylamines as energy and carbon sources. Cells were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive. Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl.\r\nPhylogenetic tree reconstructions based on 16S rRNA and concatenated alignment of broadly\r\nconserved protein-coding genes revealed its close relation to Methanosarcina mazei S-6\r\nT (similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate and the type strain of M.mazei was 98.5%, which is higher than the values recommended for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation of JL01 with S. associata GLS2T showed the methane production without any additional carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative genes involved in methanochondroithin catabolism.","lang":"eng"}],"title":"Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T","oa_version":"Published Version","publication_status":"published","file_date_updated":"2024-03-20T08:05:46Z","quality_controlled":"1","acknowledgement":"The work was supported by of Russian Foundation of Basic Research: grant № 19-04-00831 for Viktoria Shcherbakova and Olga Troshina, grant № 18-34-00334 for Viktoriia Oshurkova and Vladimir Trubitsyn. \r\nWe thank Dr Natalia Suzina (IBPM RAS, Federal Research Center Pushchino Center for\r\nBiological Research RAS) for the help with the microscopic studies, respectively; Dr. Margarita Meyer (Division of Genetics, Department of Medicine, BWH and HMS, USA) and Dr Fedor Kondrashov (IST, Austria) for their help in obtaining the genomic sequence of strain JL01. ","_id":"15071","date_created":"2024-03-04T11:41:31Z","author":[{"first_name":"Viktoriia","last_name":"Oshurkova","full_name":"Oshurkova, Viktoriia"},{"first_name":"Olga","last_name":"Troshina","full_name":"Troshina, Olga"},{"full_name":"Trubitsyn, Vladimir","last_name":"Trubitsyn","first_name":"Vladimir"},{"last_name":"Ryzhmanova","first_name":"Yana","full_name":"Ryzhmanova, Yana"},{"full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639"},{"first_name":"Viktoria","last_name":"Shcherbakova","full_name":"Shcherbakova, Viktoria"}],"doi":"10.3390/ecm2020-07116","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, and V. Shcherbakova, “Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T,” in <i>Proceedings of 1st International Electronic Conference on Microbiology</i>, Virtual, 2020.","ista":"Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. 2020. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. Proceedings of 1st International Electronic Conference on Microbiology. ECM: Electronic Conference on Microbiology.","apa":"Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O., &#38; Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In <i>Proceedings of 1st International Electronic Conference on Microbiology</i>. Virtual: MDPI. <a href=\"https://doi.org/10.3390/ecm2020-07116\">https://doi.org/10.3390/ecm2020-07116</a>","mla":"Oshurkova, Viktoriia, et al. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” <i>Proceedings of 1st International Electronic Conference on Microbiology</i>, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ecm2020-07116\">10.3390/ecm2020-07116</a>.","chicago":"Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova, Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” In <i>Proceedings of 1st International Electronic Conference on Microbiology</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ecm2020-07116\">https://doi.org/10.3390/ecm2020-07116</a>.","short":"V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V. Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology, MDPI, 2020.","ama":"Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In: <i>Proceedings of 1st International Electronic Conference on Microbiology</i>. MDPI; 2020. doi:<a href=\"https://doi.org/10.3390/ecm2020-07116\">10.3390/ecm2020-07116</a>"},"date_published":"2020-11-02T00:00:00Z","oa":1,"language":[{"iso":"eng"}],"ddc":["570"],"file":[{"relation":"main_file","file_id":"15127","date_created":"2024-03-20T08:05:46Z","file_name":"2020_ECM_Oshurkova.pdf","checksum":"d1914af7811a21a4b2744eb51b5834e3","creator":"dernst","access_level":"open_access","content_type":"application/pdf","date_updated":"2024-03-20T08:05:46Z","file_size":595543,"success":1}],"date_updated":"2024-03-20T08:06:22Z","status":"public","has_accepted_license":"1","department":[{"_id":"FyKo"}],"publication":"Proceedings of 1st International Electronic Conference on Microbiology","article_processing_charge":"Yes","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"year":"2020","type":"conference","month":"11","publisher":"MDPI","conference":{"end_date":"2020-11-30","name":"ECM: Electronic Conference on Microbiology","start_date":"2020-11-02","location":"Virtual"},"day":"02"},{"date_updated":"2025-07-10T11:57:02Z","related_material":{"record":[{"relation":"original","status":"public","id":"8321"}]},"language":[{"iso":"eng"}],"article_processing_charge":"No","publication":"Molecular Biology","department":[{"_id":"FyKo"}],"isi":1,"external_id":{"isi":["000562110300001"]},"status":"public","type":"journal_article","year":"2020","day":"19","issue":"4","publisher":"Springer Nature","month":"08","publication_status":"published","oa_version":"None","title":"Expanding the genetic code: Unnatural base pairs in biological systems","abstract":[{"lang":"eng","text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications."}],"quality_controlled":"1","page":"475-484","publication_identifier":{"issn":["0026-8933"],"eissn":["1608-3245"]},"volume":54,"article_type":"original","intvolume":"        54","acknowledgement":"We would like to thank our co-workers and members of the Alkalaeva lab for participating in discussions about the topics covered in this essay.","date_published":"2020-08-19T00:00:00Z","citation":{"ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 54(4), 475–484.","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” <i>Molecular Biology</i>, vol. 54, no. 4. Springer Nature, pp. 475–484, 2020.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molecular Biology 54 (2020) 475–484.","chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” <i>Molecular Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1134/S0026893320040111\">https://doi.org/10.1134/S0026893320040111</a>.","mla":"Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.” <i>Molecular Biology</i>, vol. 54, no. 4, Springer Nature, 2020, pp. 475–84, doi:<a href=\"https://doi.org/10.1134/S0026893320040111\">10.1134/S0026893320040111</a>.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molecular Biology</i>. 2020;54(4):475-484. doi:<a href=\"https://doi.org/10.1134/S0026893320040111\">10.1134/S0026893320040111</a>","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., &#38; Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S0026893320040111\">https://doi.org/10.1134/S0026893320040111</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"S. A.","last_name":"Mukba","full_name":"Mukba, S. A."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","full_name":"Vlasov, Petr","last_name":"Vlasov","first_name":"Petr"},{"first_name":"P. M.","last_name":"Kolosov","full_name":"Kolosov, P. M."},{"first_name":"E. Y.","last_name":"Shuvalova","full_name":"Shuvalova, E. Y."},{"last_name":"Egorova","first_name":"T. V.","full_name":"Egorova, T. V."},{"full_name":"Alkalaeva, E. Z.","first_name":"E. Z.","last_name":"Alkalaeva"}],"doi":"10.1134/S0026893320040111","date_created":"2020-08-30T22:01:11Z","_id":"8320","scopus_import":"1"},{"intvolume":"        54","publication_identifier":{"issn":["0026-8984"]},"volume":54,"article_type":"original","_id":"8321","scopus_import":"1","doi":"10.31857/S0026898420040126","date_created":"2020-08-30T22:01:11Z","author":[{"full_name":"Mukba, S. A.","last_name":"Mukba","first_name":"S. A."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","full_name":"Vlasov, Petr","last_name":"Vlasov","first_name":"Petr"},{"full_name":"Kolosov, P. M.","first_name":"P. M.","last_name":"Kolosov"},{"full_name":"Shuvalova, E. Y.","first_name":"E. Y.","last_name":"Shuvalova"},{"last_name":"Egorova","first_name":"T. V.","full_name":"Egorova, T. V."},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-07-01T00:00:00Z","citation":{"chicago":"Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.” <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences, 2020. <a href=\"https://doi.org/10.31857/S0026898420040126\">https://doi.org/10.31857/S0026898420040126</a>.","mla":"Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in biological systems.” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 4, Russian Academy of Sciences, 2020, pp. 531–41, doi:<a href=\"https://doi.org/10.31857/S0026898420040126\">10.31857/S0026898420040126</a>.","short":"S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 531–541.","ama":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molekuliarnaia biologiia</i>. 2020;54(4):531-541. doi:<a href=\"https://doi.org/10.31857/S0026898420040126\">10.31857/S0026898420040126</a>","apa":"Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., &#38; Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences. <a href=\"https://doi.org/10.31857/S0026898420040126\">https://doi.org/10.31857/S0026898420040126</a>","ista":"Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 54(4), 531–541.","ieee":"S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological systems,” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 4. Russian Academy of Sciences, pp. 531–541, 2020."},"pmid":1,"abstract":[{"text":"The genetic code is considered to use five nucleic bases (adenine, guanine, cytosine, thymine and uracil), which form two pairs for encoding information in DNA and two pairs for encoding information in RNA. Nevertheless, in recent years several artificial base pairs have been developed in attempts to expand the genetic code. Employment of these additional base pairs increases the information capacity and variety of DNA sequences, and provides a platform for the site-specific, enzymatic incorporation of extra functional components into DNA and RNA. As a result, of the development of such expanded systems, many artificial base pairs have been synthesized and tested under various conditions. Following many stages of enhancement, unnatural base pairs have been modified to eliminate their weak points, qualifying them for specific research needs. Moreover, the first attempts to create a semi-synthetic organism containing DNA with unnatural base pairs seem to have been successful. This further extends the possible applications of these kinds of pairs. Herein, we describe the most significant qualities of unnatural base pairs and their actual applications.","lang":"eng"}],"title":"Expanding the genetic code: Unnatural base pairs in biological systems","oa_version":"None","publication_status":"published","page":"531-541","quality_controlled":"1","year":"2020","type":"journal_article","month":"07","publisher":"Russian Academy of Sciences","issue":"4","day":"01","related_material":{"record":[{"relation":"translation","id":"8320","status":"public"}]},"language":[{"iso":"rus"}],"date_updated":"2025-07-10T11:57:03Z","status":"public","external_id":{"pmid":["32799218"]},"publication":"Molekuliarnaia biologiia","department":[{"_id":"FyKo"}],"article_processing_charge":"No"},{"intvolume":"        36","acknowledgement":"This work was supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement 335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute of Science and Technology. The work was started at the School of Molecular and Theoretical Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman Scientists Support Grant in Centre for Genomic Regulation (CRG). ","volume":36,"publication_identifier":{"issn":["1367-4803"],"eissn":["1460-2059"]},"article_type":"original","_id":"8645","scopus_import":"1","author":[{"last_name":"Esteban","first_name":"Laura A","full_name":"Esteban, Laura A"},{"last_name":"Lonishin","first_name":"Lyubov R","full_name":"Lonishin, Lyubov R"},{"full_name":"Bobrovskiy, Daniil M","first_name":"Daniil M","last_name":"Bobrovskiy"},{"first_name":"Gregory","last_name":"Leleytner","full_name":"Leleytner, Gregory"},{"last_name":"Bogatyreva","first_name":"Natalya S","full_name":"Bogatyreva, Natalya S"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"first_name":"Dmitry N ","last_name":"Ivankov","full_name":"Ivankov, Dmitry N "}],"doi":"10.1093/bioinformatics/btz841","date_created":"2020-10-11T22:01:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_published":"2020-03-15T00:00:00Z","citation":{"ama":"Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. <i>Bioinformatics</i>. 2020;36(6):1960-1962. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btz841\">10.1093/bioinformatics/btz841</a>","mla":"Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” <i>Bioinformatics</i>, vol. 36, no. 6, Oxford University Press, 2020, pp. 1960–62, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btz841\">10.1093/bioinformatics/btz841</a>.","short":"L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva, F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.","chicago":"Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N  Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.” <i>Bioinformatics</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/bioinformatics/btz841\">https://doi.org/10.1093/bioinformatics/btz841</a>.","apa":"Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., &#38; Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btz841\">https://doi.org/10.1093/bioinformatics/btz841</a>","ista":"Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.","ieee":"L. A. Esteban <i>et al.</i>, “HypercubeME: Two hundred million combinatorially complete datasets from a single experiment,” <i>Bioinformatics</i>, vol. 36, no. 6. Oxford University Press, pp. 1960–1962, 2020."},"pmid":1,"abstract":[{"text":"Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference genotype, two different single mutants and a double mutant with both of the single mutations. For higher-order epistasis of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional hypercube in genotype space forming a ‘combinatorially complete dataset’. So far, only a handful of such datasets have been produced by manual curation. Concurrently, random mutagenesis experiments have produced measurements of fitness and other phenotypes in a high-throughput manner, potentially containing a number of combinatorially complete datasets. We present an effective recursive algorithm for finding all hypercube structures in random mutagenesis experimental data. To test the algorithm, we applied it to the data from a recent HIS3 protein dataset and found all 199 847 053 unique combinatorially complete genotype combinations of dimensionality ranging from 2 to 12. The algorithm may be useful for researchers looking for higher-order epistasis in their high-throughput experimental data.","lang":"eng"}],"oa_version":"Published Version","title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","publication_status":"published","page":"1960-1962","quality_controlled":"1","file_date_updated":"2020-10-12T12:02:09Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"ec_funded":1,"year":"2020","project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7","grant_number":"335980"}],"type":"journal_article","month":"03","publisher":"Oxford University Press","day":"15","issue":"6","license":"https://creativecommons.org/licenses/by-nc/4.0/","language":[{"iso":"eng"}],"date_updated":"2025-05-14T11:04:01Z","ddc":["000","570"],"file":[{"file_name":"2020_Bioinformatics_Esteban.pdf","checksum":"21d6f71839deb3b83e4a356193f72767","date_created":"2020-10-12T12:02:09Z","file_id":"8649","creator":"dernst","access_level":"open_access","relation":"main_file","file_size":308341,"date_updated":"2020-10-12T12:02:09Z","content_type":"application/pdf","success":1}],"status":"public","external_id":{"pmid":["31742320"],"isi":["000538696800054"]},"publication":"Bioinformatics","has_accepted_license":"1","department":[{"_id":"FyKo"}],"isi":1,"article_processing_charge":"No"},{"publisher":"Springer Nature","month":"09","issue":"5","day":"01","type":"journal_article","year":"2020","external_id":{"isi":["000579441200009"]},"status":"public","article_processing_charge":"No","department":[{"_id":"FyKo"}],"isi":1,"publication":"Molecular Biology","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"8701","status":"public","relation":"original"}]},"date_updated":"2025-07-10T12:01:20Z","author":[{"full_name":"Sokolova, E. E.","last_name":"Sokolova","first_name":"E. E."},{"full_name":"Vlasov, Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Vlasov"},{"full_name":"Egorova, T. V.","last_name":"Egorova","first_name":"T. V."},{"last_name":"Shuvalov","first_name":"A. V.","full_name":"Shuvalov, A. V."},{"full_name":"Alkalaeva, E. Z.","last_name":"Alkalaeva","first_name":"E. Z."}],"date_created":"2020-10-25T23:01:17Z","doi":"10.1134/S0026893320050088","scopus_import":"1","_id":"8700","citation":{"apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., &#38; Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1134/S0026893320050088\">https://doi.org/10.1134/S0026893320050088</a>","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molecular Biology</i>. 2020;54(5):739-748. doi:<a href=\"https://doi.org/10.1134/S0026893320050088\">10.1134/S0026893320050088</a>","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” <i>Molecular Biology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1134/S0026893320050088\">https://doi.org/10.1134/S0026893320050088</a>.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular Biology 54 (2020) 739–748.","mla":"Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.” <i>Molecular Biology</i>, vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:<a href=\"https://doi.org/10.1134/S0026893320050088\">10.1134/S0026893320050088</a>.","ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” <i>Molecular Biology</i>, vol. 54, no. 5. Springer Nature, pp. 739–748, 2020.","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 54(5), 739–748."},"date_published":"2020-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We would like to thank the staff of CCU Genome for sequencing, Tat’yana Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided, as well as the laboratory staff for productive discussion of the results. We also thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna Kryuchkova for the exceptional contribution to the present work.","intvolume":"        54","article_type":"original","publication_identifier":{"eissn":["1608-3245"],"issn":["0026-8933"]},"volume":54,"page":"739-748","quality_controlled":"1","abstract":[{"lang":"eng","text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency."}],"publication_status":"published","oa_version":"None","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes"},{"date_updated":"2025-07-10T12:01:20Z","related_material":{"record":[{"relation":"translation","status":"public","id":"8700"}]},"language":[{"iso":"rus"}],"publication":"Molekuliarnaia biologiia","department":[{"_id":"FyKo"}],"article_processing_charge":"No","status":"public","external_id":{"pmid":["33009793"]},"year":"2020","type":"journal_article","issue":"5","day":"01","month":"09","publisher":"Russian Academy of Sciences","oa_version":"None","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","publication_status":"published","abstract":[{"lang":"eng","text":"Translation termination is a finishing step of protein biosynthesis. The significant role in this process belongs not only to protein factors of translation termination but also to the nearest nucleotide environment of stop codons. There are numerous descriptions of stop codons readthrough, which is due to specific nucleotide sequences behind them. However, represented data are segmental and don’t explain the mechanism of the nucleotide context influence on translation termination. It is well known that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for G/C-rich genes, which is related to an expression level of these genes. We investigated the connection between a frequency of nucleotides occurrence in 3' area of stop codons in the human genome and their influence on translation termination efficiency. We found that 3' context motif, which is cognate to the sequence of a stop codon, stimulates translation termination. At the same time, the nucleotide composition of 3' sequence that differs from stop codon, decreases translation termination efficiency."}],"pmid":1,"quality_controlled":"1","page":"837-848","volume":54,"publication_identifier":{"issn":["0026-8984"]},"article_type":"original","intvolume":"        54","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-09-01T00:00:00Z","citation":{"ieee":"E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva, “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes,” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 5. Russian Academy of Sciences, pp. 837–848, 2020.","ista":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848.","apa":"Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., &#38; Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences. <a href=\"https://doi.org/10.31857/S0026898420050080\">https://doi.org/10.31857/S0026898420050080</a>","ama":"Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. <i>Molekuliarnaia biologiia</i>. 2020;54(5):837-848. doi:<a href=\"https://doi.org/10.31857/S0026898420050080\">10.31857/S0026898420050080</a>","mla":"Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” <i>Molekuliarnaia biologiia</i>, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48, doi:<a href=\"https://doi.org/10.31857/S0026898420050080\">10.31857/S0026898420050080</a>.","chicago":"Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.” <i>Molekuliarnaia biologiia</i>. Russian Academy of Sciences, 2020. <a href=\"https://doi.org/10.31857/S0026898420050080\">https://doi.org/10.31857/S0026898420050080</a>.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848."},"_id":"8701","scopus_import":"1","author":[{"full_name":"Sokolova, E. E.","first_name":"E. E.","last_name":"Sokolova"},{"first_name":"Petr","last_name":"Vlasov","full_name":"Vlasov, Petr","id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"T. V.","last_name":"Egorova","full_name":"Egorova, T. V."},{"first_name":"A. V.","last_name":"Shuvalov","full_name":"Shuvalov, A. V."},{"first_name":"E. Z.","last_name":"Alkalaeva","full_name":"Alkalaeva, E. Z."}],"doi":"10.31857/S0026898420050080","date_created":"2020-10-25T23:01:17Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"type":"journal_article","year":"2020","publisher":"IOP Publishing","month":"02","day":"24","issue":"3","language":[{"iso":"eng"}],"date_updated":"2026-04-02T14:22:29Z","ddc":["530"],"file":[{"relation":"main_file","access_level":"open_access","creator":"dernst","file_name":"2020_EuropJourPhysics_Plesch.pdf","checksum":"47dda164e33b6c0c6c3ed14aad298376","file_id":"7641","date_created":"2020-04-06T08:53:53Z","file_size":1533672,"date_updated":"2020-07-14T12:48:01Z","content_type":"application/pdf"}],"article_number":"034001","external_id":{"isi":["000537425400001"],"arxiv":["1910.03290"]},"status":"public","article_processing_charge":"No","isi":1,"has_accepted_license":"1","department":[{"_id":"FyKo"}],"publication":"European Journal of Physics","intvolume":"        41","article_type":"original","publication_identifier":{"eissn":["1361-6404"],"issn":["0143-0807"]},"volume":41,"doi":"10.1088/1361-6404/ab6414","date_created":"2020-03-31T11:25:04Z","author":[{"full_name":"Plesch, Martin","first_name":"Martin","last_name":"Plesch"},{"last_name":"Plesník","first_name":"Samuel","full_name":"Plesník, Samuel"},{"first_name":"Natalia","last_name":"Ruzickova","full_name":"Ruzickova, Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"}],"scopus_import":"1","_id":"7622","arxiv":1,"citation":{"ista":"Plesch M, Plesník S, Ruzickova N. 2020. The IYPT and the ‘Ring Oiler’ problem. European Journal of Physics. 41(3), 034001.","ieee":"M. Plesch, S. Plesník, and N. Ruzickova, “The IYPT and the ‘Ring Oiler’ problem,” <i>European Journal of Physics</i>, vol. 41, no. 3. IOP Publishing, 2020.","mla":"Plesch, Martin, et al. “The IYPT and the ‘Ring Oiler’ Problem.” <i>European Journal of Physics</i>, vol. 41, no. 3, 034001, IOP Publishing, 2020, doi:<a href=\"https://doi.org/10.1088/1361-6404/ab6414\">10.1088/1361-6404/ab6414</a>.","chicago":"Plesch, Martin, Samuel Plesník, and Natalia Ruzickova. “The IYPT and the ‘Ring Oiler’ Problem.” <i>European Journal of Physics</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/1361-6404/ab6414\">https://doi.org/10.1088/1361-6404/ab6414</a>.","short":"M. Plesch, S. Plesník, N. Ruzickova, European Journal of Physics 41 (2020).","ama":"Plesch M, Plesník S, Ruzickova N. The IYPT and the “Ring Oiler” problem. <i>European Journal of Physics</i>. 2020;41(3). doi:<a href=\"https://doi.org/10.1088/1361-6404/ab6414\">10.1088/1361-6404/ab6414</a>","apa":"Plesch, M., Plesník, S., &#38; Ruzickova, N. (2020). The IYPT and the “Ring Oiler” problem. <i>European Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6404/ab6414\">https://doi.org/10.1088/1361-6404/ab6414</a>"},"oa":1,"date_published":"2020-02-24T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"lang":"eng","text":"The International Young Physicists' Tournament (IYPT) continued in 2018 in Beijing, China and 2019 in Warsaw, Poland with its 31st and 32nd editions. The IYPT is a modern scientific competition for teams of high school students, also known as the Physics World Cup. It involves long-term theoretical and experimental work focused on solving 17 publicly announced open-ended problems in teams of five. On top of that, teams have to present their solutions in front of other teams and a scientific jury, and get opposed and reviewed by their peers. Here we present a brief information about the competition with a specific focus on one of the IYPT 2018 tasks, the 'Ring Oiler'. This seemingly simple mechanical problem appeared to be of such a complexity that even the dozens of participating teams and jurying scientists were not able to solve all of its subtleties."}],"publication_status":"published","title":"The IYPT and the 'Ring Oiler' problem","oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:01Z","quality_controlled":"1"},{"file":[{"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"7947","date_created":"2020-06-08T06:27:32Z","checksum":"099e51611a5b7ca04244d03b2faddf33","file_name":"2020_ScientificReports_Uroshlev.pdf","content_type":"application/pdf","file_size":1001724,"date_updated":"2020-07-14T12:48:05Z"}],"ddc":["570"],"date_updated":"2026-04-03T09:26:06Z","language":[{"iso":"eng"}],"publication":"Scientific Reports","department":[{"_id":"FyKo"}],"isi":1,"has_accepted_license":"1","article_processing_charge":"No","status":"public","external_id":{"pmid":["32451390"],"isi":["000560774200007"]},"article_number":"8635","year":"2020","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"25","month":"05","publisher":"Springer Nature","oa_version":"Published Version","title":"A method for identification of the methylation level of CpG islands from NGS data","publication_status":"published","pmid":1,"abstract":[{"lang":"eng","text":"In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data."}],"quality_controlled":"1","file_date_updated":"2020-07-14T12:48:05Z","publication_identifier":{"eissn":["2045-2322"]},"volume":10,"article_type":"original","intvolume":"        10","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"date_published":"2020-05-25T00:00:00Z","citation":{"apa":"Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-65406-1\">https://doi.org/10.1038/s41598-020-65406-1</a>","chicago":"Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” <i>Scientific Reports</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41598-020-65406-1\">https://doi.org/10.1038/s41598-020-65406-1</a>.","short":"L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020).","mla":"Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” <i>Scientific Reports</i>, vol. 10, 8635, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41598-020-65406-1\">10.1038/s41598-020-65406-1</a>.","ama":"Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. <i>Scientific Reports</i>. 2020;10. doi:<a href=\"https://doi.org/10.1038/s41598-020-65406-1\">10.1038/s41598-020-65406-1</a>","ieee":"L. A. Uroshlev <i>et al.</i>, “A method for identification of the methylation level of CpG islands from NGS data,” <i>Scientific Reports</i>, vol. 10. Springer Nature, 2020.","ista":"Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635."},"_id":"7931","scopus_import":"1","doi":"10.1038/s41598-020-65406-1","author":[{"full_name":"Uroshlev, Leonid A.","first_name":"Leonid A.","last_name":"Uroshlev"},{"last_name":"Abdullaev","first_name":"Eldar T.","full_name":"Abdullaev, Eldar T."},{"last_name":"Umarova","first_name":"Iren R.","full_name":"Umarova, Iren R."},{"first_name":"Irina A.","last_name":"Il’Icheva","full_name":"Il’Icheva, Irina A."},{"full_name":"Panchenko, Larisa A.","last_name":"Panchenko","first_name":"Larisa A."},{"full_name":"Polozov, Robert V.","last_name":"Polozov","first_name":"Robert V."},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yury D.","last_name":"Nechipurenko","full_name":"Nechipurenko, Yury D."},{"full_name":"Grokhovsky, Sergei L.","first_name":"Sergei L.","last_name":"Grokhovsky"}],"date_created":"2020-06-07T22:00:51Z"},{"article_type":"original","volume":11,"publication_identifier":{"eissn":["1664-462X"]},"intvolume":"        11","citation":{"apa":"Nimeth, B. A., Riegler, S., &#38; Kalyna, M. (2020). Alternative splicing and DNA damage response in plants. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2020.00091\">https://doi.org/10.3389/fpls.2020.00091</a>","chicago":"Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fpls.2020.00091\">https://doi.org/10.3389/fpls.2020.00091</a>.","short":"B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).","mla":"Nimeth, Barbara Anna, et al. “Alternative Splicing and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>, vol. 11, 91, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2020.00091\">10.3389/fpls.2020.00091</a>.","ama":"Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response in plants. <i>Frontiers in Plant Science</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fpls.2020.00091\">10.3389/fpls.2020.00091</a>","ieee":"B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage response in plants,” <i>Frontiers in Plant Science</i>, vol. 11. Frontiers, 2020.","ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91."},"oa":1,"date_published":"2020-02-19T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.3389/fpls.2020.00091","date_created":"2020-03-22T23:00:46Z","author":[{"last_name":"Nimeth","first_name":"Barbara Anna","full_name":"Nimeth, Barbara Anna"},{"last_name":"Riegler","orcid":"0000-0003-3413-1343","first_name":"Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","full_name":"Riegler, Stefan"},{"last_name":"Kalyna","first_name":"Maria","full_name":"Kalyna, Maria"}],"scopus_import":"1","_id":"7603","publication_status":"published","title":"Alternative splicing and DNA damage response in plants","oa_version":"Published Version","abstract":[{"text":"Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:01Z","quality_controlled":"1","type":"journal_article","year":"2020","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"19","publisher":"Frontiers","month":"02","file":[{"file_id":"7607","file_name":"2020_FrontiersPlants_Nimeth.pdf","date_created":"2020-03-23T09:03:40Z","checksum":"57c37209f7b6712ced86c0f11b2be74e","creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:48:01Z","file_size":507414}],"ddc":["580"],"date_updated":"2026-04-16T08:28:17Z","language":[{"iso":"eng"}],"article_processing_charge":"No","has_accepted_license":"1","department":[{"_id":"FyKo"}],"isi":1,"publication":"Frontiers in Plant Science","article_number":"91","external_id":{"isi":["000518903600001"]},"status":"public"},{"related_material":{"link":[{"url":"https://doi.org/10.1038/s41587-020-0578-0","relation":"erratum"}]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-03-02T23:30:03Z","file_size":1180086,"content_type":"application/pdf","embargo":"2021-03-01","relation":"main_file","file_id":"8316","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","checksum":"1b30467500ec6277229a875b06e196d0","date_created":"2020-08-28T08:57:07Z","access_level":"open_access","creator":"dernst"}],"date_updated":"2025-04-14T07:49:47Z","ddc":["570"],"status":"public","external_id":{"isi":["000529298800003"],"pmid":["32341562"]},"publication":"Nature Biotechnology","department":[{"_id":"FyKo"}],"has_accepted_license":"1","isi":1,"article_processing_charge":"No","ec_funded":1,"year":"2020","project":[{"grant_number":"771209","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","month":"04","publisher":"Springer Nature","day":"27","pmid":1,"abstract":[{"lang":"eng","text":"Autoluminescent plants engineered to express a bacterial bioluminescence gene cluster in plastids have not been widely adopted because of low light output. We engineered tobacco plants with a fungal bioluminescence system that converts caffeic acid (present in all plants) into luciferin and report self-sustained luminescence that is visible to the naked eye. Our findings could underpin development of a suite of imaging tools for plants."}],"title":"Plants with genetically encoded autoluminescence","oa_version":"Submitted Version","publication_status":"published","page":"944-946","file_date_updated":"2021-03-02T23:30:03Z","quality_controlled":"1","intvolume":"        38","acknowledgement":"This study was designed, performed and funded by Planta LLC. We thank K. Wood for assisting in manuscript development. Planta acknowledges support from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography equipment. The Synthetic Biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial College Research Fellowship. Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL. This project received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S. acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of some of the plasmids was supported by Russian Science Foundation grant 19-74-10102. Imaging experiments were partially supported by Russian Science Foundation grant 17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which performed the sequencing and bioinformatic analysis.","volume":38,"publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"article_type":"original","_id":"7889","scopus_import":"1","date_created":"2020-05-25T15:02:00Z","author":[{"full_name":"Mitiouchkina, Tatiana","first_name":"Tatiana","last_name":"Mitiouchkina"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"full_name":"Gonzalez Somermeyer, Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa","orcid":"0000-0001-9139-5383","last_name":"Gonzalez Somermeyer"},{"full_name":"Markina, Nadezhda M.","last_name":"Markina","first_name":"Nadezhda M."},{"first_name":"Tatiana V.","last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V."},{"first_name":"Elena B.","last_name":"Guglya","full_name":"Guglya, Elena B."},{"full_name":"Karataeva, Tatiana A.","first_name":"Tatiana A.","last_name":"Karataeva"},{"first_name":"Kseniia A.","last_name":"Palkina","full_name":"Palkina, Kseniia A."},{"full_name":"Shakhova, Ekaterina S.","last_name":"Shakhova","first_name":"Ekaterina S."},{"full_name":"Fakhranurova, Liliia I.","first_name":"Liliia I.","last_name":"Fakhranurova"},{"first_name":"Sofia V.","last_name":"Chekova","full_name":"Chekova, Sofia V."},{"last_name":"Tsarkova","first_name":"Aleksandra S.","full_name":"Tsarkova, Aleksandra S."},{"full_name":"Golubev, Yaroslav V.","last_name":"Golubev","first_name":"Yaroslav V."},{"first_name":"Vadim V.","last_name":"Negrebetsky","full_name":"Negrebetsky, Vadim V."},{"full_name":"Dolgushin, Sergey A.","first_name":"Sergey A.","last_name":"Dolgushin"},{"full_name":"Shalaev, Pavel V.","last_name":"Shalaev","first_name":"Pavel V."},{"full_name":"Shlykov, Dmitry","last_name":"Shlykov","first_name":"Dmitry"},{"first_name":"Olesya A.","last_name":"Melnik","full_name":"Melnik, Olesya A."},{"full_name":"Shipunova, Victoria O.","last_name":"Shipunova","first_name":"Victoria O."},{"full_name":"Deyev, Sergey M.","first_name":"Sergey M.","last_name":"Deyev"},{"full_name":"Bubyrev, Andrey I.","last_name":"Bubyrev","first_name":"Andrey I."},{"full_name":"Pushin, Alexander S.","last_name":"Pushin","first_name":"Alexander S."},{"first_name":"Vladimir V.","last_name":"Choob","full_name":"Choob, Vladimir V."},{"full_name":"Dolgov, Sergey V.","last_name":"Dolgov","first_name":"Sergey V."},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yampolsky","first_name":"Ilia V.","full_name":"Yampolsky, Ilia V."},{"full_name":"Sarkisyan, Karen S.","first_name":"Karen S.","last_name":"Sarkisyan"}],"doi":"10.1038/s41587-020-0500-9","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"date_published":"2020-04-27T00:00:00Z","citation":{"ista":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.","ieee":"T. Mitiouchkina <i>et al.</i>, “Plants with genetically encoded autoluminescence,” <i>Nature Biotechnology</i>, vol. 38. Springer Nature, pp. 944–946, 2020.","ama":"Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically encoded autoluminescence. <i>Nature Biotechnology</i>. 2020;38:944-946. doi:<a href=\"https://doi.org/10.1038/s41587-020-0500-9\">10.1038/s41587-020-0500-9</a>","short":"T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V. Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova, S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V. Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S. Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan, Nature Biotechnology 38 (2020) 944–946.","mla":"Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.” <i>Nature Biotechnology</i>, vol. 38, Springer Nature, 2020, pp. 944–46, doi:<a href=\"https://doi.org/10.1038/s41587-020-0500-9\">10.1038/s41587-020-0500-9</a>.","chicago":"Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.” <i>Nature Biotechnology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41587-020-0500-9\">https://doi.org/10.1038/s41587-020-0500-9</a>.","apa":"Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-020-0500-9\">https://doi.org/10.1038/s41587-020-0500-9</a>"}},{"doi":"10.1038/s41588-020-00712-y","date_created":"2020-10-25T23:01:20Z","author":[{"full_name":" Galan, Silvia","first_name":"Silvia","last_name":" Galan"},{"id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","full_name":"Machnik, Nick N","last_name":"Machnik","orcid":"0000-0001-6617-9742","first_name":"Nick N"},{"last_name":"Kruse","first_name":"Kai","full_name":"Kruse, Kai"},{"full_name":"Díaz, Noelia","first_name":"Noelia","last_name":"Díaz"},{"full_name":"Marti-Renom, Marc A","first_name":"Marc A","last_name":"Marti-Renom"},{"full_name":"Vaquerizas, Juan M","last_name":"Vaquerizas","first_name":"Juan M"}],"scopus_import":"1","OA_place":"repository","_id":"8707","citation":{"ieee":"S.  Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M. Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction,” <i>Nature Genetics</i>, vol. 52. Springer Nature, pp. 1247–1255, 2020.","ista":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 52, 1247–1255.","apa":"Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., &#38; Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. <i>Nature Genetics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41588-020-00712-y\">https://doi.org/10.1038/s41588-020-00712-y</a>","chicago":"Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” <i>Nature Genetics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41588-020-00712-y\">https://doi.org/10.1038/s41588-020-00712-y</a>.","short":"S.  Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas, Nature Genetics 52 (2020) 1247–1255.","mla":"Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.” <i>Nature Genetics</i>, vol. 52, Springer Nature, 2020, pp. 1247–55, doi:<a href=\"https://doi.org/10.1038/s41588-020-00712-y\">10.1038/s41588-020-00712-y</a>.","ama":"Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. <i>Nature Genetics</i>. 2020;52:1247-1255. doi:<a href=\"https://doi.org/10.1038/s41588-020-00712-y\">10.1038/s41588-020-00712-y</a>"},"date_published":"2020-10-19T00:00:00Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Work in the Vaquerizas laboratory is funded by the Max Planck Society, the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN to J.M.V.) and the Medical Research Council in the UK. This research was partially funded by the European Union’s H2020 Framework Programme through the European Research Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R. The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia, Innovación y Universidades to the European Molecular Biology Laboratory partnership, the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from the European Regional Development Fund corresponding to the 2014–2020 Smart Growth Operating Program. S.G. thanks the support from the Company of Biologists (grant no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship programme.","intvolume":"        52","article_type":"original","volume":52,"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"page":"1247-1255","main_file_link":[{"open_access":"1","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7610641/"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Dynamic changes in the three-dimensional (3D) organization of chromatin are associated with central biological processes, such as transcription, replication and development. Therefore, the comprehensive identification and quantification of these changes is fundamental to understanding of evolutionary and regulatory mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity (CHESS), an algorithm for the comparison of chromatin contact maps and automatic differential feature extraction. We demonstrate the robustness of CHESS to experimental variability and showcase its biological applications on (1) interspecies comparisons of syntenic regions in human and mouse models; (2) intraspecies identification of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and (4) the systematic identification of chromatin contact differences in high-resolution Capture-C data. In summary, CHESS is a computationally efficient method for the comparison and classification of changes in chromatin contact data."}],"pmid":1,"publication_status":"published","title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","oa_version":"Submitted Version","publisher":"Springer Nature","month":"10","OA_type":"green","day":"19","type":"journal_article","year":"2020","external_id":{"pmid":["33077914"],"isi":["000579693500004"]},"status":"public","article_processing_charge":"No","isi":1,"department":[{"_id":"FyKo"}],"publication":"Nature Genetics","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"18642","relation":"dissertation_contains"}]},"date_updated":"2026-06-06T22:30:29Z"},{"month":"07","publisher":"Springer Nature","issue":"7","day":"01","year":"2019","type":"journal_article","status":"public","external_id":{"isi":["000480348200017"]},"isi":1,"department":[{"_id":"FyKo"}],"publication":"Nature Microbiology","article_processing_charge":"No","language":[{"iso":"eng"}],"date_updated":"2023-08-28T08:39:47Z","scopus_import":"1","_id":"6506","date_created":"2019-05-29T13:03:30Z","doi":"10.1038/s41564-019-0412-y","author":[{"first_name":"Lianet","last_name":"Noda-García","full_name":"Noda-García, Lianet"},{"full_name":"Davidi, Dan","first_name":"Dan","last_name":"Davidi"},{"last_name":"Korenblum","first_name":"Elisa","full_name":"Korenblum, Elisa"},{"last_name":"Elazar","first_name":"Assaf","full_name":"Elazar, Assaf"},{"id":"2EF67C84-F248-11E8-B48F-1D18A9856A87","full_name":"Putintseva, Ekaterina","last_name":"Putintseva","first_name":"Ekaterina"},{"first_name":"Asaph","last_name":"Aharoni","full_name":"Aharoni, Asaph"},{"full_name":"Tawfik, Dan S.","first_name":"Dan S.","last_name":"Tawfik"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., &#38; Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-019-0412-y\">https://doi.org/10.1038/s41564-019-0412-y</a>","ama":"Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. <i>Nature Microbiology</i>. 2019;4(7):1221–1230. doi:<a href=\"https://doi.org/10.1038/s41564-019-0412-y\">10.1038/s41564-019-0412-y</a>","chicago":"Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” <i>Nature Microbiology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41564-019-0412-y\">https://doi.org/10.1038/s41564-019-0412-y</a>.","mla":"Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” <i>Nature Microbiology</i>, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:<a href=\"https://doi.org/10.1038/s41564-019-0412-y\">10.1038/s41564-019-0412-y</a>.","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.","ieee":"L. Noda-García <i>et al.</i>, “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” <i>Nature Microbiology</i>, vol. 4, no. 7. Springer Nature, pp. 1221–1230, 2019.","ista":"Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 4(7), 1221–1230."},"oa":1,"date_published":"2019-07-01T00:00:00Z","intvolume":"         4","article_type":"original","publication_identifier":{"issn":["2058-5276"]},"volume":4,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/340828v2"}],"page":"1221–1230","quality_controlled":"1","abstract":[{"text":"How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele.","lang":"eng"}],"oa_version":"Preprint","title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments","publication_status":"published"},{"external_id":{"isi":["000500748900021"],"pmid":["31792410"]},"status":"public","article_processing_charge":"No","publication":"Nature Biotechnology","isi":1,"department":[{"_id":"FyKo"}],"related_material":{"record":[{"status":"public","id":"13059","relation":"research_data"}]},"language":[{"iso":"eng"}],"date_updated":"2025-07-10T11:54:19Z","publisher":"Springer Nature","month":"12","issue":"12","day":"01","ec_funded":1,"project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","year":"2019","page":"1466-1470","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/","open_access":"1"}],"quality_controlled":"1","pmid":1,"abstract":[{"lang":"eng","text":"Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods start by aligning the most similar sequences and subsequently incorporate the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy declines substantially as the number of sequences is scaled up5. We introduce a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard workstation and substantially improves accuracy on datasets larger than 10,000 sequences. Our regressive algorithm works the other way around to the progressive algorithm and begins by aligning the most dissimilar sequences. It uses an efficient divide-and-conquer strategy to run third-party alignment methods in linear time, regardless of their original complexity. Our approach will enable analyses of extremely large genomic datasets such as the recently announced Earth BioGenome Project, which comprises 1.5 million eukaryotic genomes6."}],"publication_status":"published","oa_version":"Submitted Version","title":"Large multiple sequence alignments with a root-to-leaf regressive method","author":[{"last_name":"Garriga","first_name":"Edgar","full_name":"Garriga, Edgar"},{"full_name":"Di Tommaso, Paolo","last_name":"Di Tommaso","first_name":"Paolo"},{"last_name":"Magis","first_name":"Cedrik","full_name":"Magis, Cedrik"},{"full_name":"Erb, Ionas","first_name":"Ionas","last_name":"Erb"},{"full_name":"Mansouri, Leila","last_name":"Mansouri","first_name":"Leila"},{"last_name":"Baltzis","first_name":"Athanasios","full_name":"Baltzis, Athanasios"},{"first_name":"Hafid","last_name":"Laayouni","full_name":"Laayouni, Hafid"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"full_name":"Floden, Evan","last_name":"Floden","first_name":"Evan"},{"full_name":"Notredame, Cedric","last_name":"Notredame","first_name":"Cedric"}],"date_created":"2019-12-15T23:00:43Z","doi":"10.1038/s41587-019-0333-6","_id":"7181","scopus_import":"1","oa":1,"date_published":"2019-12-01T00:00:00Z","citation":{"ista":"Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.","ieee":"E. Garriga <i>et al.</i>, “Large multiple sequence alignments with a root-to-leaf regressive method,” <i>Nature Biotechnology</i>, vol. 37, no. 12. Springer Nature, pp. 1466–1470, 2019.","mla":"Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” <i>Nature Biotechnology</i>, vol. 37, no. 12, Springer Nature, 2019, pp. 1466–70, doi:<a href=\"https://doi.org/10.1038/s41587-019-0333-6\">10.1038/s41587-019-0333-6</a>.","chicago":"Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” <i>Nature Biotechnology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41587-019-0333-6\">https://doi.org/10.1038/s41587-019-0333-6</a>.","short":"E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019) 1466–1470.","ama":"Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. <i>Nature Biotechnology</i>. 2019;37(12):1466-1470. doi:<a href=\"https://doi.org/10.1038/s41587-019-0333-6\">10.1038/s41587-019-0333-6</a>","apa":"Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-019-0333-6\">https://doi.org/10.1038/s41587-019-0333-6</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        37","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"volume":37,"article_type":"original"},{"abstract":[{"lang":"eng","text":"OGs with putative pseudogenes by the number of affected genomes in different chlamydial species. Frameshift and nonsense mutations located less than 60 bp upstreamof the gene end or present in a single genome from the corresponding OG were excluded. (CSV 31 kb)"}],"related_material":{"record":[{"status":"public","id":"6898","relation":"used_in_publication"}]},"title":"Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","oa_version":"Published Version","date_updated":"2026-04-03T09:39:40Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808772.v1"}],"status":"public","department":[{"_id":"FyKo"}],"article_processing_charge":"No","year":"2019","type":"research_data_reference","month":"09","_id":"9731","publisher":"Springer Nature","date_created":"2021-07-27T14:09:11Z","author":[{"full_name":"Sigalova, Olga","last_name":"Sigalova","first_name":"Olga"},{"full_name":"Chaplin, Andrei","last_name":"Chaplin","first_name":"Andrei"},{"first_name":"Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva","full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"full_name":"Shelyakin, Pavel","first_name":"Pavel","last_name":"Shelyakin"},{"last_name":"Filaretov","first_name":"Vsevolod","full_name":"Filaretov, Vsevolod"},{"last_name":"Akkuratov","first_name":"Evgeny","full_name":"Akkuratov, Evgeny"},{"last_name":"Burskaia","first_name":"Valentina","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"doi":"10.6084/m9.figshare.9808772.v1","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"12","citation":{"chicago":"Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9808772.v1\">https://doi.org/10.6084/m9.figshare.9808772.v1</a>.","mla":"Sigalova, Olga, et al. <i>Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808772.v1\">10.6084/m9.figshare.9808772.v1</a>.","short":"O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ama":"Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808772.v1\">10.6084/m9.figshare.9808772.v1</a>","apa":"Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov, E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808772.v1\">https://doi.org/10.6084/m9.figshare.9808772.v1</a>","ista":"Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E, Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808772.v1\">10.6084/m9.figshare.9808772.v1</a>.","ieee":"O. Sigalova <i>et al.</i>, “Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019."},"date_published":"2019-09-12T00:00:00Z","oa":1},{"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808760.v1","open_access":"1"}],"status":"public","article_processing_charge":"No","department":[{"_id":"FyKo"}],"related_material":{"record":[{"status":"public","id":"6898","relation":"used_in_publication"}]},"abstract":[{"lang":"eng","text":"Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For the analysis of putative pseudogenes, events located less than 60 bp. away from gene end or present in a single genome from the corresponding OG were excluded. (CSV 600 kb)"}],"date_updated":"2026-04-03T09:39:40Z","title":"Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","oa_version":"Published Version","author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"orcid":"0000-0003-1006-6639","last_name":"Bochkareva","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga"},{"full_name":"Shelyakin, Pavel V.","last_name":"Shelyakin","first_name":"Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"date_created":"2021-08-06T07:59:56Z","doi":"10.6084/m9.figshare.9808760.v1","publisher":"Springer Nature","_id":"9783","month":"09","oa":1,"date_published":"2019-09-12T00:00:00Z","citation":{"apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808760.v1\">https://doi.org/10.6084/m9.figshare.9808760.v1</a>","mla":"Sigalova, Olga M., et al. <i>Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808760.v1\">10.6084/m9.figshare.9808760.v1</a>.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9808760.v1\">https://doi.org/10.6084/m9.figshare.9808760.v1</a>.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808760.v1\">10.6084/m9.figshare.9808760.v1</a>","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808760.v1\">10.6084/m9.figshare.9808760.v1</a>."},"day":"12","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","year":"2019"},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"abstract":[{"text":"Distribution of OGs with mosaic phyletic patterns across species (complete genomes only). (CSV 7 kb)","lang":"eng"}],"date_updated":"2026-04-03T09:39:40Z","oa_version":"Published Version","title":"Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808802.v1","open_access":"1"}],"status":"public","article_processing_charge":"No","department":[{"_id":"FyKo"}],"type":"research_data_reference","year":"2019","date_created":"2021-08-11T14:26:40Z","doi":"10.6084/m9.figshare.9808802.v1","author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"full_name":"Chaplin, Andrei V.","first_name":"Andrei V.","last_name":"Chaplin"},{"first_name":"Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva","full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"publisher":"Springer Nature","_id":"9890","month":"09","oa":1,"date_published":"2019-09-12T00:00:00Z","citation":{"short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","mla":"Sigalova, Olga M., et al. <i>Additional File 15 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808802.v1\">10.6084/m9.figshare.9808802.v1</a>.","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 15 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9808802.v1\">https://doi.org/10.6084/m9.figshare.9808802.v1</a>.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808802.v1\">10.6084/m9.figshare.9808802.v1</a>","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808802.v1\">https://doi.org/10.6084/m9.figshare.9808802.v1</a>","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808802.v1\">10.6084/m9.figshare.9808802.v1</a>.","ieee":"O. M. 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