[{"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."}],"status":"public","intvolume":"        54","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>Molekuliarnaia biologiia</i>. Russian Academy of Sciences. <a href=\"https://doi.org/10.31857/S0026898420050080\">https://doi.org/10.31857/S0026898420050080</a>","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.","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>.","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>.","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.","short":"E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia biologiia 54 (2020) 837–848.","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>"},"day":"01","article_type":"original","publication_status":"published","title":"The influence of A/G composition of 3' stop codon contexts on translation termination efficiency in eukaryotes","related_material":{"record":[{"relation":"translation","status":"public","id":"8700"}]},"_id":"8701","month":"09","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","department":[{"_id":"FyKo"}],"volume":54,"date_updated":"2023-08-22T10:39:37Z","date_created":"2020-10-25T23:01:17Z","year":"2020","quality_controlled":"1","page":"837-848","pmid":1,"scopus_import":"1","publication_identifier":{"issn":["00268984"]},"article_processing_charge":"No","type":"journal_article","language":[{"iso":"rus"}],"publisher":"Russian Academy of Sciences","doi":"10.31857/S0026898420050080","author":[{"last_name":"Sokolova","first_name":"E. E.","full_name":"Sokolova, E. E."},{"id":"38BB9AC4-F248-11E8-B48F-1D18A9856A87","last_name":"Vlasov","full_name":"Vlasov, Petr","first_name":"Petr"},{"full_name":"Egorova, T. V.","first_name":"T. V.","last_name":"Egorova"},{"last_name":"Shuvalov","full_name":"Shuvalov, A. V.","first_name":"A. V."},{"last_name":"Alkalaeva","first_name":"E. Z.","full_name":"Alkalaeva, E. Z."}],"publication":"Molekuliarnaia biologiia","issue":"5","date_published":"2020-09-01T00:00:00Z","oa_version":"None","external_id":{"pmid":["33009793"]}},{"department":[{"_id":"FyKo"}],"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.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"10","_id":"8707","article_type":"original","title":"CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction","publication_status":"published","day":"19","intvolume":"        52","citation":{"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>","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>.","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.","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>.","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>"},"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."}],"status":"public","date_published":"2020-10-19T00:00:00Z","oa_version":"None","external_id":{"isi":["000579693500004"],"pmid":["33077914"]},"author":[{"last_name":" Galan","full_name":" Galan, Silvia","first_name":"Silvia"},{"id":"3591A0AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6617-9742","last_name":"Machnik","full_name":"Machnik, Nick N","first_name":"Nick N"},{"full_name":"Kruse, Kai","first_name":"Kai","last_name":"Kruse"},{"first_name":"Noelia","full_name":"Díaz, Noelia","last_name":"Díaz"},{"full_name":"Marti-Renom, Marc A","first_name":"Marc A","last_name":"Marti-Renom"},{"full_name":"Vaquerizas, Juan M","first_name":"Juan M","last_name":"Vaquerizas"}],"publication":"Nature Genetics","publisher":"Springer Nature","doi":"10.1038/s41588-020-00712-y","type":"journal_article","language":[{"iso":"eng"}],"article_processing_charge":"No","scopus_import":"1","pmid":1,"publication_identifier":{"eissn":["15461718"],"issn":["10614036"]},"date_updated":"2023-08-22T10:37:10Z","quality_controlled":"1","page":"1247-1255","date_created":"2020-10-25T23:01:20Z","year":"2020","volume":52,"isi":1},{"intvolume":"        11","citation":{"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>.","ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91.","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>","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.","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>.","short":"B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).","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>"},"day":"19","has_accepted_license":"1","status":"public","article_number":"91","abstract":[{"lang":"eng","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."}],"department":[{"_id":"FyKo"}],"publication_status":"published","title":"Alternative splicing and DNA damage response in plants","oa":1,"article_type":"original","month":"02","_id":"7603","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1664462X"]},"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","isi":1,"file":[{"relation":"main_file","checksum":"57c37209f7b6712ced86c0f11b2be74e","file_size":507414,"creator":"dernst","file_name":"2020_FrontiersPlants_Nimeth.pdf","file_id":"7607","date_created":"2020-03-23T09:03:40Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:01Z"}],"volume":11,"date_created":"2020-03-22T23:00:46Z","year":"2020","quality_controlled":"1","date_updated":"2023-08-18T07:05:18Z","publication":"Frontiers in Plant Science","author":[{"last_name":"Nimeth","full_name":"Nimeth, Barbara Anna","first_name":"Barbara Anna"},{"full_name":"Riegler, Stefan","first_name":"Stefan","last_name":"Riegler","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","orcid":"0000-0003-3413-1343"},{"full_name":"Kalyna, Maria","first_name":"Maria","last_name":"Kalyna"}],"ddc":["580"],"oa_version":"Published Version","external_id":{"isi":["000518903600001"]},"date_published":"2020-02-19T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:48:01Z","doi":"10.3389/fpls.2020.00091","publisher":"Frontiers"},{"department":[{"_id":"FyKo"}],"article_type":"original","title":"The IYPT and the 'Ring Oiler' problem","oa":1,"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7622","month":"02","citation":{"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>.","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.","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>.","ista":"Plesch M, Plesník S, Ruzickova N. 2020. The IYPT and the ‘Ring Oiler’ problem. European Journal of Physics. 41(3), 034001.","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>","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>","short":"M. Plesch, S. Plesník, N. Ruzickova, European Journal of Physics 41 (2020)."},"intvolume":"        41","has_accepted_license":"1","day":"24","abstract":[{"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.","lang":"eng"}],"article_number":"034001","status":"public","ddc":["530"],"author":[{"last_name":"Plesch","full_name":"Plesch, Martin","first_name":"Martin"},{"last_name":"Plesník","full_name":"Plesník, Samuel","first_name":"Samuel"},{"last_name":"Ruzickova","full_name":"Ruzickova, Natalia","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425"}],"publication":"European Journal of Physics","issue":"3","date_published":"2020-02-24T00:00:00Z","external_id":{"arxiv":["1910.03290"],"isi":["000537425400001"]},"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:01Z","type":"journal_article","arxiv":1,"language":[{"iso":"eng"}],"publisher":"IOP Publishing","doi":"10.1088/1361-6404/ab6414","scopus_import":"1","publication_identifier":{"issn":["01430807"],"eissn":["13616404"]},"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":41,"file":[{"checksum":"47dda164e33b6c0c6c3ed14aad298376","relation":"main_file","creator":"dernst","file_size":1533672,"file_name":"2020_EuropJourPhysics_Plesch.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-06T08:53:53Z","file_id":"7641","content_type":"application/pdf"}],"isi":1,"date_updated":"2023-08-18T10:18:29Z","quality_controlled":"1","year":"2020","date_created":"2020-03-31T11:25:04Z"},{"department":[{"_id":"FyKo"}],"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.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"04","_id":"7889","title":"Plants with genetically encoded autoluminescence","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41587-020-0578-0"}]},"oa":1,"publication_status":"published","article_type":"original","day":"27","has_accepted_license":"1","intvolume":"        38","citation":{"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>","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.","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>.","ieee":"T. Mitiouchkina <i>et al.</i>, “Plants with genetically encoded autoluminescence,” <i>Nature Biotechnology</i>, vol. 38. Springer Nature, pp. 944–946, 2020.","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.","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>"},"ec_funded":1,"status":"public","abstract":[{"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.","lang":"eng"}],"external_id":{"isi":["000529298800003"],"pmid":["32341562"]},"oa_version":"Submitted Version","date_published":"2020-04-27T00:00:00Z","publication":"Nature Biotechnology","ddc":["570"],"author":[{"first_name":"Tatiana","full_name":"Mitiouchkina, Tatiana","last_name":"Mitiouchkina"},{"first_name":"Alexander S.","full_name":"Mishin, Alexander S.","last_name":"Mishin"},{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9139-5383","last_name":"Gonzalez Somermeyer","first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa"},{"last_name":"Markina","first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M."},{"last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V."},{"last_name":"Guglya","first_name":"Elena B.","full_name":"Guglya, Elena B."},{"last_name":"Karataeva","first_name":"Tatiana A.","full_name":"Karataeva, Tatiana A."},{"last_name":"Palkina","full_name":"Palkina, Kseniia A.","first_name":"Kseniia A."},{"last_name":"Shakhova","first_name":"Ekaterina S.","full_name":"Shakhova, Ekaterina S."},{"first_name":"Liliia I.","full_name":"Fakhranurova, Liliia I.","last_name":"Fakhranurova"},{"last_name":"Chekova","full_name":"Chekova, Sofia V.","first_name":"Sofia V."},{"last_name":"Tsarkova","first_name":"Aleksandra S.","full_name":"Tsarkova, Aleksandra S."},{"last_name":"Golubev","first_name":"Yaroslav V.","full_name":"Golubev, Yaroslav V."},{"last_name":"Negrebetsky","first_name":"Vadim V.","full_name":"Negrebetsky, Vadim V."},{"last_name":"Dolgushin","first_name":"Sergey A.","full_name":"Dolgushin, Sergey A."},{"first_name":"Pavel V.","full_name":"Shalaev, Pavel V.","last_name":"Shalaev"},{"full_name":"Shlykov, Dmitry","first_name":"Dmitry","last_name":"Shlykov"},{"first_name":"Olesya A.","full_name":"Melnik, Olesya A.","last_name":"Melnik"},{"full_name":"Shipunova, Victoria O.","first_name":"Victoria O.","last_name":"Shipunova"},{"first_name":"Sergey M.","full_name":"Deyev, Sergey M.","last_name":"Deyev"},{"last_name":"Bubyrev","full_name":"Bubyrev, Andrey I.","first_name":"Andrey I."},{"last_name":"Pushin","first_name":"Alexander S.","full_name":"Pushin, Alexander S."},{"full_name":"Choob, Vladimir V.","first_name":"Vladimir V.","last_name":"Choob"},{"last_name":"Dolgov","full_name":"Dolgov, Sergey V.","first_name":"Sergey V."},{"last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"last_name":"Yampolsky","full_name":"Yampolsky, Ilia V.","first_name":"Ilia V."},{"full_name":"Sarkisyan, Karen S.","first_name":"Karen S.","last_name":"Sarkisyan"}],"doi":"10.1038/s41587-020-0500-9","publisher":"Springer Nature","language":[{"iso":"eng"}],"file_date_updated":"2021-03-02T23:30:03Z","type":"journal_article","article_processing_charge":"No","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"scopus_import":"1","pmid":1,"quality_controlled":"1","page":"944-946","date_created":"2020-05-25T15:02:00Z","year":"2020","date_updated":"2023-09-05T15:30:34Z","project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","call_identifier":"H2020"}],"volume":38,"file":[{"date_created":"2020-08-28T08:57:07Z","content_type":"application/pdf","file_id":"8316","access_level":"open_access","date_updated":"2021-03-02T23:30:03Z","file_name":"2020_NatureBiotech_Mitiouchkina.pdf","embargo":"2021-03-01","file_size":1180086,"creator":"dernst","relation":"main_file","checksum":"1b30467500ec6277229a875b06e196d0"}],"isi":1},{"volume":10,"file":[{"date_updated":"2020-07-14T12:48:05Z","access_level":"open_access","date_created":"2020-06-08T06:27:32Z","content_type":"application/pdf","file_id":"7947","file_name":"2020_ScientificReports_Uroshlev.pdf","creator":"dernst","file_size":1001724,"checksum":"099e51611a5b7ca04244d03b2faddf33","relation":"main_file"}],"isi":1,"quality_controlled":"1","date_created":"2020-06-07T22:00:51Z","year":"2020","date_updated":"2023-08-21T07:00:17Z","publication_identifier":{"eissn":["20452322"]},"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:05Z","type":"journal_article","doi":"10.1038/s41598-020-65406-1","publisher":"Springer Nature","publication":"Scientific Reports","ddc":["570"],"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."},{"full_name":"Umarova, Iren R.","first_name":"Iren R.","last_name":"Umarova"},{"full_name":"Il’Icheva, Irina A.","first_name":"Irina A.","last_name":"Il’Icheva"},{"last_name":"Panchenko","full_name":"Panchenko, Larisa A.","first_name":"Larisa A."},{"first_name":"Robert V.","full_name":"Polozov, Robert V.","last_name":"Polozov"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"},{"first_name":"Yury D.","full_name":"Nechipurenko, Yury D.","last_name":"Nechipurenko"},{"first_name":"Sergei L.","full_name":"Grokhovsky, Sergei L.","last_name":"Grokhovsky"}],"external_id":{"isi":["000560774200007"]},"oa_version":"Published Version","date_published":"2020-05-25T00:00:00Z","article_number":"8635","status":"public","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."}],"intvolume":"        10","citation":{"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>","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).","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.","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>.","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.","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>."},"day":"25","has_accepted_license":"1","oa":1,"title":"A method for identification of the methylation level of CpG islands from NGS data","publication_status":"published","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7931","month":"05","department":[{"_id":"FyKo"}]},{"isi":1,"volume":37,"project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"date_updated":"2023-09-06T14:32:52Z","year":"2019","date_created":"2019-12-15T23:00:43Z","quality_controlled":"1","page":"1466-1470","pmid":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/","open_access":"1"}],"scopus_import":"1","publication_identifier":{"eissn":["15461696"],"issn":["10870156"]},"article_processing_charge":"No","type":"journal_article","language":[{"iso":"eng"}],"publisher":"Springer Nature","doi":"10.1038/s41587-019-0333-6","author":[{"last_name":"Garriga","first_name":"Edgar","full_name":"Garriga, Edgar"},{"first_name":"Paolo","full_name":"Di Tommaso, Paolo","last_name":"Di Tommaso"},{"last_name":"Magis","full_name":"Magis, Cedrik","first_name":"Cedrik"},{"last_name":"Erb","full_name":"Erb, Ionas","first_name":"Ionas"},{"first_name":"Leila","full_name":"Mansouri, Leila","last_name":"Mansouri"},{"last_name":"Baltzis","full_name":"Baltzis, Athanasios","first_name":"Athanasios"},{"last_name":"Laayouni","first_name":"Hafid","full_name":"Laayouni, Hafid"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"},{"first_name":"Evan","full_name":"Floden, Evan","last_name":"Floden"},{"first_name":"Cedric","full_name":"Notredame, Cedric","last_name":"Notredame"}],"issue":"12","publication":"Nature Biotechnology","date_published":"2019-12-01T00:00:00Z","oa_version":"Submitted Version","external_id":{"pmid":["31792410"],"isi":["000500748900021"]},"abstract":[{"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.","lang":"eng"}],"status":"public","ec_funded":1,"intvolume":"        37","citation":{"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>","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.","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>.","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>.","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>"},"day":"01","article_type":"original","publication_status":"published","title":"Large multiple sequence alignments with a root-to-leaf regressive method","related_material":{"record":[{"id":"13059","relation":"research_data","status":"public"}]},"oa":1,"month":"12","_id":"7181","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"FyKo"}]},{"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:30Z","type":"journal_article","doi":"10.1371/journal.pgen.1008079","publisher":"Public Library of Science","publication":"PLoS Genetics","issue":"4","ddc":["570"],"author":[{"last_name":"Pokusaeva","full_name":"Pokusaeva, Victoria","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X"},{"last_name":"Usmanova","full_name":"Usmanova, Dinara R.","first_name":"Dinara R."},{"last_name":"Putintseva","first_name":"Ekaterina V.","full_name":"Putintseva, Ekaterina V."},{"full_name":"Espinar, Lorena","first_name":"Lorena","last_name":"Espinar"},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","first_name":"Karen","last_name":"Sarkisyan"},{"full_name":"Mishin, Alexander S.","first_name":"Alexander S.","last_name":"Mishin"},{"first_name":"Natalya S.","full_name":"Bogatyreva, Natalya S.","last_name":"Bogatyreva"},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","last_name":"Ivankov","first_name":"Dmitry","full_name":"Ivankov, Dmitry"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy"},{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","full_name":"Avvakumov, Sergey","last_name":"Avvakumov"},{"first_name":"Inna S.","full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya"},{"full_name":"Filion, Guillaume J.","first_name":"Guillaume J.","last_name":"Filion"},{"last_name":"Carey","first_name":"Lucas B.","full_name":"Carey, Lucas B."},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"}],"oa_version":"Published Version","external_id":{"isi":["000466866000029"]},"date_published":"2019-04-10T00:00:00Z","volume":15,"isi":1,"file":[{"creator":"dernst","file_size":3726017,"checksum":"cf3889c8a8a16053dacf9c3776cbe217","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:30Z","content_type":"application/pdf","file_id":"6445","date_created":"2019-05-14T08:26:08Z","file_name":"2019_PLOSGenetics_Pokusaeva.pdf"}],"quality_controlled":"1","year":"2019","date_created":"2019-05-13T07:58:38Z","date_updated":"2023-08-25T10:30:37Z","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_identifier":{"eissn":["15537404"]},"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"article_processing_charge":"No","title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","related_material":{"record":[{"id":"9789","status":"public","relation":"research_data"},{"id":"9790","relation":"research_data","status":"public"},{"id":"9797","status":"public","relation":"research_data"}]},"oa":1,"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6419","month":"04","department":[{"_id":"FyKo"}],"article_number":"e1008079","status":"public","abstract":[{"text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible.","lang":"eng"}],"ec_funded":1,"intvolume":"        15","citation":{"ieee":"V. Pokusaeva <i>et al.</i>, “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” <i>PLoS Genetics</i>, vol. 15, no. 4. Public Library of Science, 2019.","mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” <i>PLoS Genetics</i>, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079\">10.1371/journal.pgen.1008079</a>.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1008079\">https://doi.org/10.1371/journal.pgen.1008079</a>","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” <i>PLoS Genetics</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pgen.1008079\">https://doi.org/10.1371/journal.pgen.1008079</a>.","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. <i>PLoS Genetics</i>. 2019;15(4). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079\">10.1371/journal.pgen.1008079</a>","short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019)."},"day":"10","has_accepted_license":"1"},{"language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1038/s41564-019-0412-y","publisher":"Springer Nature","publication":"Nature Microbiology","issue":"7","author":[{"last_name":"Noda-García","full_name":"Noda-García, Lianet","first_name":"Lianet"},{"first_name":"Dan","full_name":"Davidi, Dan","last_name":"Davidi"},{"first_name":"Elisa","full_name":"Korenblum, Elisa","last_name":"Korenblum"},{"full_name":"Elazar, Assaf","first_name":"Assaf","last_name":"Elazar"},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina","first_name":"Ekaterina","id":"2EF67C84-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Aharoni","full_name":"Aharoni, Asaph","first_name":"Asaph"},{"last_name":"Tawfik","full_name":"Tawfik, Dan S.","first_name":"Dan S."}],"external_id":{"isi":["000480348200017"]},"oa_version":"Preprint","date_published":"2019-07-01T00:00:00Z","volume":4,"isi":1,"quality_controlled":"1","page":"1221–1230","date_created":"2019-05-29T13:03:30Z","year":"2019","date_updated":"2023-08-28T08:39:47Z","publication_identifier":{"issn":["2058-5276"]},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/340828v2"}],"article_processing_charge":"No","title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments","oa":1,"publication_status":"published","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6506","month":"07","department":[{"_id":"FyKo"}],"status":"public","abstract":[{"lang":"eng","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."}],"intvolume":"         4","citation":{"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>","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.","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>.","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.","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>","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>."},"day":"01"},{"scopus_import":"1","publication_identifier":{"eissn":["14712164"]},"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":20,"file":[{"content_type":"application/pdf","date_created":"2019-10-01T10:33:17Z","file_id":"6924","access_level":"open_access","date_updated":"2020-07-14T12:47:44Z","file_name":"2019_BioMed_Sigalova.pdf","file_size":4157175,"creator":"kschuh","relation":"main_file","checksum":"b798773c5823012d31c812c9f7975da2"}],"isi":1,"date_updated":"2023-08-30T06:20:22Z","quality_controlled":"1","date_created":"2019-09-22T22:00:36Z","year":"2019","ddc":["570"],"author":[{"full_name":"Sigalova, Olga M.","first_name":"Olga M.","last_name":"Sigalova"},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","first_name":"Olga","full_name":"Bochkareva, Olga","last_name":"Bochkareva"},{"last_name":"Shelyakin","full_name":"Shelyakin, Pavel V.","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"},{"last_name":"Burskaia","full_name":"Burskaia, Valentina","first_name":"Valentina"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"publication":"BMC Genomics","issue":"1","date_published":"2019-09-12T00:00:00Z","external_id":{"isi":["000485256100001"]},"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:44Z","type":"journal_article","language":[{"iso":"eng"}],"publisher":"BioMed Central","doi":"10.1186/s12864-019-6059-5","citation":{"chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>. BioMed Central, 2019. <a href=\"https://doi.org/10.1186/s12864-019-6059-5\">https://doi.org/10.1186/s12864-019-6059-5</a>.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 20(1), 710.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s12864-019-6059-5\">https://doi.org/10.1186/s12864-019-6059-5</a>","ieee":"O. M. Sigalova <i>et al.</i>, “Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction,” <i>BMC Genomics</i>, vol. 20, no. 1. BioMed Central, 2019.","mla":"Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>, vol. 20, no. 1, 710, BioMed Central, 2019, doi:<a href=\"https://doi.org/10.1186/s12864-019-6059-5\">10.1186/s12864-019-6059-5</a>.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019).","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. <i>BMC Genomics</i>. 2019;20(1). doi:<a href=\"https://doi.org/10.1186/s12864-019-6059-5\">10.1186/s12864-019-6059-5</a>"},"intvolume":"        20","has_accepted_license":"1","day":"12","abstract":[{"lang":"eng","text":"Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity."}],"article_number":"710","status":"public","department":[{"_id":"FyKo"}],"title":"Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","related_material":{"record":[{"id":"9731","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9783"},{"id":"9890","status":"public","relation":"research_data"},{"id":"9892","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9893"},{"id":"9894","relation":"research_data","status":"public"},{"id":"9895","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9896"},{"status":"public","relation":"research_data","id":"9897"},{"status":"public","relation":"research_data","id":"9898"},{"status":"public","relation":"research_data","id":"9899"},{"relation":"research_data","status":"public","id":"9900"},{"id":"9901","status":"public","relation":"research_data"}]},"oa":1,"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6898","month":"09"},{"status":"public","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)"}],"date_created":"2021-07-27T14:09:11Z","year":"2019","date_updated":"2023-08-30T06:20:21Z","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808772.v1","open_access":"1"}],"citation":{"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>","short":"O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","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>.","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.","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>.","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>","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>."},"day":"12","article_processing_charge":"No","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6898"}]},"title":"Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","oa":1,"type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.6084/m9.figshare.9808772.v1","_id":"9731","month":"09","publisher":"Springer Nature","author":[{"first_name":"Olga","full_name":"Sigalova, Olga","last_name":"Sigalova"},{"last_name":"Chaplin","full_name":"Chaplin, Andrei","first_name":"Andrei"},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","first_name":"Olga","full_name":"Bochkareva, Olga","last_name":"Bochkareva"},{"last_name":"Shelyakin","first_name":"Pavel","full_name":"Shelyakin, Pavel"},{"last_name":"Filaretov","full_name":"Filaretov, Vsevolod","first_name":"Vsevolod"},{"last_name":"Akkuratov","first_name":"Evgeny","full_name":"Akkuratov, Evgeny"},{"last_name":"Burskaia","full_name":"Burskaia, Valentina","first_name":"Valentina"},{"first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S.","last_name":"Gelfand"}],"oa_version":"Published Version","date_published":"2019-09-12T00:00:00Z","department":[{"_id":"FyKo"}]},{"article_processing_charge":"No","day":"12","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808760.v1","open_access":"1"}],"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).","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>","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>","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>.","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>.","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.","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>."},"date_updated":"2023-08-30T06:20:21Z","date_created":"2021-08-06T07:59:56Z","year":"2019","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)"}],"status":"public","date_published":"2019-09-12T00:00:00Z","department":[{"_id":"FyKo"}],"oa_version":"Published Version","author":[{"first_name":"Olga M.","full_name":"Sigalova, Olga M.","last_name":"Sigalova"},{"full_name":"Chaplin, Andrei V.","first_name":"Andrei V.","last_name":"Chaplin"},{"orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga","full_name":"Bochkareva, Olga"},{"last_name":"Shelyakin","first_name":"Pavel V.","full_name":"Shelyakin, Pavel V."},{"first_name":"Vsevolod A.","full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov"},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"last_name":"Burskaia","first_name":"Valentina","full_name":"Burskaia, Valentina"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"publisher":"Springer Nature","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9783","month":"09","doi":"10.6084/m9.figshare.9808760.v1","type":"research_data_reference","related_material":{"record":[{"id":"6898","status":"public","relation":"used_in_publication"}]},"title":"Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","oa":1},{"citation":{"chicago":"Pokusaeva, Victoria, Dinara R. 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