[{"language":[{"iso":"eng"}],"keyword":["Public Health","Environmental and Occupational Health"],"month":"10","article_number":"ckad160.597","oa_version":"Published Version","publication":"European Journal of Public Health","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"14882","checksum":"98706755bb4cc5d553818ade7660a7d2","file_size":71057,"date_created":"2024-01-24T11:12:33Z","file_name":"2023_EurJourPublicHealth_Rella.pdf","content_type":"application/pdf","date_updated":"2024-01-24T11:12:33Z"}],"oa":1,"publication_identifier":{"issn":["1101-1262"],"eissn":["1464-360X"]},"date_published":"2023-10-01T00:00:00Z","type":"conference_abstract","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"publisher":"Oxford University Press","file_date_updated":"2024-01-24T11:12:33Z","quality_controlled":"1","title":"Complex vaccination strategies prevent the emergence of vaccine resistance","intvolume":"        33","publication_status":"published","article_processing_charge":"No","date_created":"2024-01-22T12:02:28Z","department":[{"_id":"GaTk"}],"author":[{"full_name":"Rella, Simon","first_name":"Simon","last_name":"Rella","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425"},{"last_name":"Kulikova","first_name":"Y","full_name":"Kulikova, Y"},{"id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","full_name":"Minnegalieva, Aygul","last_name":"Minnegalieva","first_name":"Aygul"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"issue":"Supplement_2","_id":"14862","ddc":["570"],"volume":33,"doi":"10.1093/eurpub/ckad160.597","day":"01","date_updated":"2024-01-24T11:16:09Z","citation":{"ista":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination strategies prevent the emergence of vaccine resistance. European Journal of Public Health. vol. 33, ckad160.597.","mla":"Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” <i>European Journal of Public Health</i>, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">10.1093/eurpub/ckad160.597</a>.","short":"S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.","chicago":"Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In <i>European Journal of Public Health</i>, Vol. 33. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">https://doi.org/10.1093/eurpub/ckad160.597</a>.","ieee":"S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in <i>European Journal of Public Health</i>, 2023, vol. 33, no. Supplement_2.","apa":"Rella, S., Kulikova, Y., Minnegalieva, A., &#38; Kondrashov, F. (2023). Complex vaccination strategies prevent the emergence of vaccine resistance. In <i>European Journal of Public Health</i> (Vol. 33). Oxford University Press. <a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">https://doi.org/10.1093/eurpub/ckad160.597</a>","ama":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. In: <i>European Journal of Public Health</i>. Vol 33. Oxford University Press; 2023. doi:<a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">10.1093/eurpub/ckad160.597</a>"},"year":"2023"},{"file":[{"file_size":1555006,"checksum":"d6165f41c7f1c2c04b04256ec9f003fb","date_created":"2023-06-26T10:26:04Z","content_type":"application/pdf","file_name":"2023_NatureComm_Gert.pdf","date_updated":"2023-06-26T10:26:04Z","access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"13172"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2041-1723"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-06-14T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","month":"06","article_number":"3506","publication":"Nature Communications","has_accepted_license":"1","volume":14,"acknowledgement":"We thank Manfred Schartl for sharing RNA-seq data from medaka ovaries and testes prior to publication; Maria Novatchkova for help with RNA-seq analysis; Katharina Lust for advice on medaka techniques; Milan Malinsky for input on Lake Malawi cichlid Bouncer sequences; Felicia Spitzer, Mirjam Binner, and Anna Bandura for help with genotyping; Friedrich Puhl, Kerstin Rattner, Julia Koenig, and Dijana Sunjic for taking care of zebrafish and medaka; and the Pauli lab for helpful discussions about the project and feedback on the manuscript. K.R.B.G. was supported by a DOC Fellowship from the Austrian Academy of Sciences. Work in the Pauli lab was supported by the FWF START program (Y 1031-B28 to A.P.), the ERC CoG 101044495/GaMe, the HFSP Career Development Award (CDA00066/2015 to A.P.), a HFSP Young Investigator Award (RGY0079/2020 to A.P.) and the FWF SFB RNA-Deco (project number F80). The IMP receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). Work by J.S. and Y.M. in this project was supported by the Israel Science Foundation grant 636/21 to Y.M. Work by L.J. was supported by the Swedish Research Council grant 2020-04936 and the Knut and Alice Wallenberg Foundation grant 2018.0042. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission.","ddc":["570"],"doi":"10.1038/s41467-023-39317-4","day":"14","abstract":[{"lang":"eng","text":"Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization."}],"date_updated":"2023-12-13T11:26:34Z","citation":{"ieee":"K. R. B. Gert <i>et al.</i>, “Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Gert, Krista R.B., Karin Panser, Joachim Surm, Benjamin S. Steinmetz, Alexander Schleiffer, Luca Jovine, Yehu Moran, Fyodor Kondrashov, and Andrea Pauli. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39317-4\">https://doi.org/10.1038/s41467-023-39317-4</a>.","apa":"Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39317-4\">https://doi.org/10.1038/s41467-023-39317-4</a>","ama":"Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39317-4\">10.1038/s41467-023-39317-4</a>","ista":"Gert KRB, Panser K, Surm J, Steinmetz BS, Schleiffer A, Jovine L, Moran Y, Kondrashov F, Pauli A. 2023. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 14, 3506.","short":"K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine, Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023).","mla":"Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” <i>Nature Communications</i>, vol. 14, 3506, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39317-4\">10.1038/s41467-023-39317-4</a>."},"year":"2023","isi":1,"external_id":{"isi":["001048208600023"]},"publisher":"Springer Nature","article_type":"original","quality_controlled":"1","file_date_updated":"2023-06-26T10:26:04Z","publication_status":"published","date_created":"2023-06-25T22:00:45Z","department":[{"_id":"FyKo"}],"article_processing_charge":"No","title":"Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries","intvolume":"        14","_id":"13164","scopus_import":"1","author":[{"full_name":"Gert, Krista R.B.","last_name":"Gert","first_name":"Krista R.B."},{"full_name":"Panser, Karin","last_name":"Panser","first_name":"Karin"},{"full_name":"Surm, Joachim","last_name":"Surm","first_name":"Joachim"},{"full_name":"Steinmetz, Benjamin S.","last_name":"Steinmetz","first_name":"Benjamin S."},{"full_name":"Schleiffer, Alexander","first_name":"Alexander","last_name":"Schleiffer"},{"full_name":"Jovine, Luca","first_name":"Luca","last_name":"Jovine"},{"last_name":"Moran","first_name":"Yehu","full_name":"Moran, Yehu"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"full_name":"Pauli, Andrea","last_name":"Pauli","first_name":"Andrea"}]},{"language":[{"iso":"eng"}],"publication":"GigaScience","month":"07","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/gigascience/giad045"}],"date_published":"2023-07-27T00:00:00Z","type":"journal_article","oa":1,"publication_identifier":{"eissn":["2047-217X"]},"quality_controlled":"1","article_type":"original","publisher":"Oxford Academic","author":[{"full_name":"Wolfsberger, Walter","first_name":"Walter","last_name":"Wolfsberger"},{"last_name":"Chhugani","first_name":"Karishma","full_name":"Chhugani, Karishma"},{"full_name":"Shchubelka, Khrystyna","last_name":"Shchubelka","first_name":"Khrystyna"},{"last_name":"Frolova","first_name":"Alina","full_name":"Frolova, Alina"},{"full_name":"Salyha, Yuriy","first_name":"Yuriy","last_name":"Salyha"},{"full_name":"Zlenko, Oksana","last_name":"Zlenko","first_name":"Oksana"},{"last_name":"Arych","first_name":"Mykhailo","full_name":"Arych, Mykhailo"},{"last_name":"Dziuba","first_name":"Dmytro","full_name":"Dziuba, Dmytro"},{"first_name":"Andrii","last_name":"Parkhomenko","full_name":"Parkhomenko, Andrii"},{"full_name":"Smolanka, Volodymyr","last_name":"Smolanka","first_name":"Volodymyr"},{"full_name":"Gümüş, Zeynep H.","last_name":"Gümüş","first_name":"Zeynep H."},{"full_name":"Sezgin, Efe","first_name":"Efe","last_name":"Sezgin"},{"last_name":"Diaz-Lameiro","first_name":"Alondra","full_name":"Diaz-Lameiro, Alondra"},{"first_name":"Viktor R.","last_name":"Toth","full_name":"Toth, Viktor R."},{"last_name":"Maci","first_name":"Megi","full_name":"Maci, Megi"},{"first_name":"Eric","last_name":"Bortz","full_name":"Bortz, Eric"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Patricia M.","last_name":"Morton","full_name":"Morton, Patricia M."},{"first_name":"Paweł P.","last_name":"Łabaj","full_name":"Łabaj, Paweł P."},{"last_name":"Romero","first_name":"Veronika","full_name":"Romero, Veronika"},{"full_name":"Hlávka, Jakub","last_name":"Hlávka","first_name":"Jakub"},{"full_name":"Mangul, Serghei","last_name":"Mangul","first_name":"Serghei"},{"first_name":"Taras K.","last_name":"Oleksyk","full_name":"Oleksyk, Taras K."}],"pmid":1,"_id":"13976","scopus_import":"1","title":"Scientists without borders: Lessons from Ukraine","intvolume":"        12","publication_status":"epub_ahead","date_created":"2023-08-06T22:01:13Z","department":[{"_id":"FyKo"}],"article_processing_charge":"Yes","volume":12,"acknowledgement":"Our article is dedicated to all freedom-loving people around the world and to the people of Ukraine who fight for our freedom. Special thanks to Anita Bandrowski, Oleksandra V. Ivashchenko, and Sanita Reinsone for the helpful review, valuable criticism, and useful suggestions while preparing this manuscript, and to Tetiana Yes'kova for helping with Ukrainian translation.\r\nAll authors volunteered their time. No funding supported work on this article.","isi":1,"external_id":{"pmid":["37496156"],"isi":["001081086100001"]},"date_updated":"2023-12-13T12:01:46Z","year":"2023","citation":{"apa":"Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko, O., … Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine. <i>GigaScience</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/gigascience/giad045\">https://doi.org/10.1093/gigascience/giad045</a>","ama":"Wolfsberger W, Chhugani K, Shchubelka K, et al. Scientists without borders: Lessons from Ukraine. <i>GigaScience</i>. 2023;12. doi:<a href=\"https://doi.org/10.1093/gigascience/giad045\">10.1093/gigascience/giad045</a>","chicago":"Wolfsberger, Walter, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova, Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, et al. “Scientists without Borders: Lessons from Ukraine.” <i>GigaScience</i>. Oxford Academic, 2023. <a href=\"https://doi.org/10.1093/gigascience/giad045\">https://doi.org/10.1093/gigascience/giad045</a>.","ieee":"W. Wolfsberger <i>et al.</i>, “Scientists without borders: Lessons from Ukraine,” <i>GigaScience</i>, vol. 12. Oxford Academic, 2023.","mla":"Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.” <i>GigaScience</i>, vol. 12, Oxford Academic, 2023, doi:<a href=\"https://doi.org/10.1093/gigascience/giad045\">10.1093/gigascience/giad045</a>.","short":"W. Wolfsberger, K. Chhugani, K. Shchubelka, A. Frolova, Y. Salyha, O. Zlenko, M. Arych, D. Dziuba, A. Parkhomenko, V. Smolanka, Z.H. Gümüş, E. Sezgin, A. Diaz-Lameiro, V.R. Toth, M. Maci, E. Bortz, F. Kondrashov, P.M. Morton, P.P. Łabaj, V. Romero, J. Hlávka, S. Mangul, T.K. Oleksyk, GigaScience 12 (2023).","ista":"Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience. 12."},"abstract":[{"text":"Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades’ worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery.","lang":"eng"}],"doi":"10.1093/gigascience/giad045","day":"27"},{"has_accepted_license":"1","publication":"PLoS ONE","oa_version":"Published Version","article_number":"e0282689","month":"03","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2023-03-16T00:00:00Z","publication_identifier":{"eissn":["1932-6203"]},"oa":1,"file":[{"access_level":"open_access","relation":"main_file","success":1,"file_id":"12771","creator":"dernst","date_created":"2023-03-27T07:09:08Z","checksum":"0281bdfccf8d76c4e08dd011c603f6b6","file_size":856625,"date_updated":"2023-03-27T07:09:08Z","content_type":"application/pdf","file_name":"2023_PLoSOne_Pak.pdf"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","_id":"12758","issue":"3","author":[{"full_name":"Pak, Marina A.","first_name":"Marina A.","last_name":"Pak"},{"full_name":"Markhieva, Karina A.","first_name":"Karina A.","last_name":"Markhieva"},{"full_name":"Novikova, Mariia S.","last_name":"Novikova","first_name":"Mariia S."},{"full_name":"Petrov, Dmitry S.","last_name":"Petrov","first_name":"Dmitry S."},{"last_name":"Vorobyev","first_name":"Ilya S.","full_name":"Vorobyev, Ilya S."},{"full_name":"Maksimova, Ekaterina","last_name":"Maksimova","first_name":"Ekaterina","id":"2FBE0DE4-F248-11E8-B48F-1D18A9856A87"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"},{"full_name":"Ivankov, Dmitry N.","last_name":"Ivankov","first_name":"Dmitry N."}],"department":[{"_id":"FyKo"},{"_id":"MaRo"}],"date_created":"2023-03-26T22:01:07Z","article_processing_charge":"No","publication_status":"published","intvolume":"        18","title":"Using AlphaFold to predict the impact of single mutations on protein stability and function","quality_controlled":"1","file_date_updated":"2023-03-27T07:09:08Z","publisher":"Public Library of Science","article_type":"original","citation":{"ista":"Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 18(3), e0282689.","short":"M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova, F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).","mla":"Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” <i>PLoS ONE</i>, vol. 18, no. 3, e0282689, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pone.0282689\">10.1371/journal.pone.0282689</a>.","chicago":"Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov, Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov. “Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability and Function.” <i>PLoS ONE</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pone.0282689\">https://doi.org/10.1371/journal.pone.0282689</a>.","ieee":"M. A. Pak <i>et al.</i>, “Using AlphaFold to predict the impact of single mutations on protein stability and function,” <i>PLoS ONE</i>, vol. 18, no. 3. Public Library of Science, 2023.","ama":"Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. <i>PLoS ONE</i>. 2023;18(3). doi:<a href=\"https://doi.org/10.1371/journal.pone.0282689\">10.1371/journal.pone.0282689</a>","apa":"Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0282689\">https://doi.org/10.1371/journal.pone.0282689</a>"},"year":"2023","date_updated":"2023-08-01T13:47:14Z","external_id":{"isi":["000985134400106"]},"isi":1,"day":"16","doi":"10.1371/journal.pone.0282689","abstract":[{"lang":"eng","text":"AlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted the pLDDT and <pLDDT> metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the same AlphaFold pLDDT metrics with the impact of a single mutation on structure using a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold may not be immediately applied to other problems or applications in protein folding."}],"volume":18,"acknowledgement":"The authors acknowledge the use of Zhores supercomputer [28] for obtaining the results presented in this paper.The authors thank Zimin Foundation and Petrovax for support of the presented study at the School of Molecular and Theoretical Biology 2021.","ddc":["570"]},{"publisher":"Springer Nature","article_type":"letter_note","quality_controlled":"1","ec_funded":1,"page":"374-380","date_created":"2022-04-17T22:01:48Z","article_processing_charge":"No","department":[{"_id":"FyKo"}],"publication_status":"published","intvolume":"        19","title":"Unlocking capacities of genomics for the COVID-19 response and future pandemics","scopus_import":"1","pmid":1,"_id":"11187","issue":"4","author":[{"last_name":"Knyazev","first_name":"Sergey","full_name":"Knyazev, Sergey"},{"last_name":"Chhugani","first_name":"Karishma","full_name":"Chhugani, Karishma"},{"last_name":"Sarwal","first_name":"Varuni","full_name":"Sarwal, Varuni"},{"first_name":"Ram","last_name":"Ayyala","full_name":"Ayyala, Ram"},{"last_name":"Singh","first_name":"Harman","full_name":"Singh, Harman"},{"full_name":"Karthikeyan, Smruthi","first_name":"Smruthi","last_name":"Karthikeyan"},{"full_name":"Deshpande, Dhrithi","last_name":"Deshpande","first_name":"Dhrithi"},{"last_name":"Baykal","first_name":"Pelin Icer","full_name":"Baykal, Pelin Icer"},{"full_name":"Comarova, Zoia","first_name":"Zoia","last_name":"Comarova"},{"last_name":"Lu","first_name":"Angela","full_name":"Lu, Angela"},{"full_name":"Porozov, Yuri","first_name":"Yuri","last_name":"Porozov"},{"first_name":"Tetyana I.","last_name":"Vasylyeva","full_name":"Vasylyeva, Tetyana I."},{"last_name":"Wertheim","first_name":"Joel O.","full_name":"Wertheim, Joel O."},{"last_name":"Tierney","first_name":"Braden T.","full_name":"Tierney, Braden T."},{"first_name":"Charles Y.","last_name":"Chiu","full_name":"Chiu, Charles Y."},{"full_name":"Sun, Ren","first_name":"Ren","last_name":"Sun"},{"last_name":"Wu","first_name":"Aiping","full_name":"Wu, Aiping"},{"first_name":"Malak S.","last_name":"Abedalthagafi","full_name":"Abedalthagafi, Malak S."},{"first_name":"Victoria M.","last_name":"Pak","full_name":"Pak, Victoria M."},{"first_name":"Shivashankar H.","last_name":"Nagaraj","full_name":"Nagaraj, Shivashankar H."},{"full_name":"Smith, Adam L.","first_name":"Adam L.","last_name":"Smith"},{"first_name":"Pavel","last_name":"Skums","full_name":"Skums, Pavel"},{"last_name":"Pasaniuc","first_name":"Bogdan","full_name":"Pasaniuc, Bogdan"},{"last_name":"Komissarov","first_name":"Andrey","full_name":"Komissarov, Andrey"},{"full_name":"Mason, Christopher E.","first_name":"Christopher E.","last_name":"Mason"},{"first_name":"Eric","last_name":"Bortz","full_name":"Bortz, Eric"},{"full_name":"Lemey, Philippe","last_name":"Lemey","first_name":"Philippe"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Beerenwinkel","first_name":"Niko","full_name":"Beerenwinkel, Niko"},{"full_name":"Lam, Tommy Tsan Yuk","last_name":"Lam","first_name":"Tommy Tsan Yuk"},{"first_name":"Nicholas C.","last_name":"Wu","full_name":"Wu, Nicholas C."},{"full_name":"Zelikovsky, Alex","first_name":"Alex","last_name":"Zelikovsky"},{"last_name":"Knight","first_name":"Rob","full_name":"Knight, Rob"},{"full_name":"Crandall, Keith A.","first_name":"Keith A.","last_name":"Crandall"},{"full_name":"Mangul, Serghei","last_name":"Mangul","first_name":"Serghei"}],"acknowledgement":"Our paper is dedicated to all freedom-loving people around the world, and to the people of Ukraine who fight for our freedom. We thank William M. Switzer and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions. We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially supported by National Science Foundation grants 2041984. T.L. is supported by the NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund (R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828. M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W. was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S. acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly supported by Molecular Basis of Disease at Georgia State University and NIH awards R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread. J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases (NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V. is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers “Digital biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395) and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the California Department of Public Health, the Innovative Genomics Institute (IGI) at the University of California, Berkeley, and University of California, San Francisco, NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project 206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C. acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported by an ERC Consolidator grant to F.K. (771209–CharFL).","volume":19,"day":"08","doi":"10.1038/s41592-022-01444-z","abstract":[{"text":"During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.","lang":"eng"}],"citation":{"chicago":"Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” <i>Nature Methods</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41592-022-01444-z\">https://doi.org/10.1038/s41592-022-01444-z</a>.","ieee":"S. Knyazev <i>et al.</i>, “Unlocking capacities of genomics for the COVID-19 response and future pandemics,” <i>Nature Methods</i>, vol. 19, no. 4. Springer Nature, pp. 374–380, 2022.","apa":"Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-022-01444-z\">https://doi.org/10.1038/s41592-022-01444-z</a>","ama":"Knyazev S, Chhugani K, Sarwal V, et al. Unlocking capacities of genomics for the COVID-19 response and future pandemics. <i>Nature Methods</i>. 2022;19(4):374-380. doi:<a href=\"https://doi.org/10.1038/s41592-022-01444-z\">10.1038/s41592-022-01444-z</a>","ista":"Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 19(4), 374–380.","mla":"Knyazev, Sergey, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.” <i>Nature Methods</i>, vol. 19, no. 4, Springer Nature, 2022, pp. 374–80, doi:<a href=\"https://doi.org/10.1038/s41592-022-01444-z\">10.1038/s41592-022-01444-z</a>.","short":"S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan, D. Deshpande, P.I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T.I. Vasylyeva, J.O. Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak, S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E. Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T.T.Y. Lam, N.C. Wu, A. Zelikovsky, R. Knight, K.A. Crandall, S. Mangul, Nature Methods 19 (2022) 374–380."},"year":"2022","date_updated":"2023-08-03T06:46:09Z","external_id":{"isi":["000781199600011"],"pmid":["35396471"]},"isi":1,"language":[{"iso":"eng"}],"project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"}],"oa_version":"Published Version","month":"04","publication":"Nature Methods","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41592-022-01444-z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"oa":1,"type":"journal_article","date_published":"2022-04-08T00:00:00Z"},{"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_created":"2022-05-02T09:05:20Z","checksum":"12601b8a5c6b83bb618f92bcb963ecc9","file_size":3564155,"date_updated":"2022-05-02T09:05:20Z","content_type":"application/pdf","file_name":"2022_ScientificReports_Dranenko.pdf","access_level":"open_access","relation":"main_file","success":1,"file_id":"11349","creator":"dernst"}],"date_published":"2022-04-27T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["2045-2322"]},"language":[{"iso":"eng"}],"publication":"Scientific Reports","has_accepted_license":"1","month":"04","article_number":"6868","oa_version":"Published Version","project":[{"_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","grant_number":"I05127","name":"Evolutionary analysis of gene regulation"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"ddc":["570"],"acknowledgement":"The project was initiated with Aygul Minnegalieva and Yulia Yakovleva at the Summer School of Molecular and Theoretical Biology (SMTB-2020), supported by the Zimin Foundation. We thank Inna Shapovalenko, Daria Abuzova, Elizaveta Kaminskaya, and Dmitriy Zvezdin for their contribution to the project during SMTB-2020. We also thank Peter Vlasov for fruitful discussions.This study was supported by the Russian Foundation for Basic Research (RFBR), Grant # 20-54-14005 and Fonds zur Förderung der wissenschaftlichen Forschung (FWF), Grant # I5127-B. The work of OB is supported by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. ","volume":12,"isi":1,"external_id":{"pmid":["35477739"],"isi":["000788639400032"]},"date_updated":"2023-08-03T06:59:49Z","citation":{"ieee":"N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” <i>Scientific Reports</i>, vol. 12. Springer Nature, 2022.","chicago":"Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” <i>Scientific Reports</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41598-022-10827-3\">https://doi.org/10.1038/s41598-022-10827-3</a>.","apa":"Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., &#38; Bochkareva, O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-022-10827-3\">https://doi.org/10.1038/s41598-022-10827-3</a>","ama":"Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. <i>Scientific Reports</i>. 2022;12. doi:<a href=\"https://doi.org/10.1038/s41598-022-10827-3\">10.1038/s41598-022-10827-3</a>","ista":"Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. 2022. Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. 12, 6868.","mla":"Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.” <i>Scientific Reports</i>, vol. 12, 6868, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41598-022-10827-3\">10.1038/s41598-022-10827-3</a>.","short":"N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific Reports 12 (2022)."},"year":"2022","abstract":[{"lang":"eng","text":"Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals."}],"doi":"10.1038/s41598-022-10827-3","day":"27","file_date_updated":"2022-05-02T09:05:20Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"Springer Nature","author":[{"first_name":"NO","last_name":"Dranenko","full_name":"Dranenko, NO"},{"full_name":"Tutukina, MN","last_name":"Tutukina","first_name":"MN"},{"full_name":"Gelfand, MS","last_name":"Gelfand","first_name":"MS"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","first_name":"Olga","last_name":"Bochkareva"}],"_id":"11344","pmid":1,"scopus_import":"1","title":"Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia","intvolume":"        12","publication_status":"published","date_created":"2022-05-02T07:08:42Z","department":[{"_id":"FyKo"}],"article_processing_charge":"No"},{"keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Bulletin of Mathematical Biology","article_number":"74","month":"06","project":[{"name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"grant_number":"I05127","name":"Evolutionary analysis of gene regulation","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f"}],"oa_version":"Published Version","status":"public","related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"date_updated":"2022-06-20T07:51:32Z","file_name":"2022_BulletinMathBiology_Saona.pdf","content_type":"application/pdf","date_created":"2022-06-20T07:51:32Z","file_size":463025,"checksum":"05a1fe7d10914a00c2bca9b447993a65","file_id":"11455","creator":"dernst","relation":"main_file","access_level":"open_access","success":1}],"type":"journal_article","date_published":"2022-06-17T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"file_date_updated":"2022-06-20T07:51:32Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"Springer Nature","issue":"8","author":[{"last_name":"Saona Urmeneta","first_name":"Raimundo J","full_name":"Saona Urmeneta, Raimundo J","orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Khudiakova","first_name":"Kseniia","full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"}],"scopus_import":"1","_id":"11447","intvolume":"        84","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"article_processing_charge":"Yes (via OA deal)","date_created":"2022-06-17T16:16:15Z","publication_status":"published","ddc":["510","570"],"acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","volume":84,"external_id":{"isi":["000812509800001"]},"isi":1,"year":"2022","citation":{"ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022.","apa":"Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. 2022;84(8). doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>"},"date_updated":"2023-08-03T07:20:53Z","abstract":[{"lang":"eng","text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks."}],"day":"17","doi":"10.1007/s11538-022-01029-z"},{"type":"journal_article","date_published":"2022-05-05T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["2050-084X"]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","file_id":"11454","relation":"main_file","access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"2022_eLife_Somermeyer.pdf","date_updated":"2022-06-20T07:44:19Z","file_size":5297213,"checksum":"7573c28f44028ab0cc81faef30039e44","date_created":"2022-06-20T07:44:19Z"}],"has_accepted_license":"1","publication":"eLife","article_number":"75842","month":"05","project":[{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"language":[{"iso":"eng"}],"external_id":{"isi":["000799197200001"]},"isi":1,"year":"2022","citation":{"short":"L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022).","mla":"Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>, vol. 11, 75842, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>.","ista":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.","ama":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>","apa":"Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>","ieee":"L. Gonzalez Somermeyer <i>et al.</i>, “Heterogeneity of the GFP fitness landscape and data-driven protein design,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","chicago":"Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>."},"date_updated":"2023-08-03T07:20:15Z","abstract":[{"lang":"eng","text":"Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering."}],"day":"05","doi":"10.7554/elife.75842","ddc":["570"],"acknowledgement":"We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova for technical assistance and data interpretation. Core facility Biomolecular Interactions and Crystallization of CEITEC Masaryk University is gratefully acknowledged for the obtaining of the scientific data presented in this paper. This research was supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF). MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility in the Vanderbilt University Center for Structural Biology. We are grateful to Joel M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4, the Imperial College Research Fellowship and the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\"). Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH). This work was supported by a Russian Science Foundation grant 19-74-10102.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385.","volume":11,"author":[{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa","last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa"},{"full_name":"Fleiss, Aubin","first_name":"Aubin","last_name":"Fleiss"},{"last_name":"Mishin","first_name":"Alexander S","full_name":"Mishin, Alexander S"},{"full_name":"Bozhanova, Nina G","last_name":"Bozhanova","first_name":"Nina G"},{"last_name":"Igolkina","first_name":"Anna A","full_name":"Igolkina, Anna A"},{"full_name":"Meiler, Jens","first_name":"Jens","last_name":"Meiler"},{"last_name":"Alaball Pujol","first_name":"Maria-Elisenda","full_name":"Alaball Pujol, Maria-Elisenda"},{"full_name":"Putintseva, Ekaterina V","first_name":"Ekaterina V","last_name":"Putintseva"},{"full_name":"Sarkisyan, Karen S","last_name":"Sarkisyan","first_name":"Karen S"},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"11448","intvolume":"        11","title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"article_processing_charge":"No","date_created":"2022-06-18T09:06:59Z","publication_status":"published","file_date_updated":"2022-06-20T07:44:19Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"eLife Sciences Publications"},{"volume":378,"external_id":{"isi":["000963463700023"]},"isi":1,"year":"2022","citation":{"mla":"Chhugani, Karishma, et al. “Remote Opportunities for Scholars in Ukraine.” <i>Science</i>, vol. 378, no. 6626, American Association for the Advancement of Science, 2022, pp. 1285–86, doi:<a href=\"https://doi.org/10.1126/science.adg0797\">10.1126/science.adg0797</a>.","short":"K. Chhugani, A. Frolova, Y. Salyha, A. Fiscutean, O. Zlenko, S. Reinsone, W.W. Wolfsberger, O.V. Ivashchenko, M. Maci, D. Dziuba, A. Parkhomenko, E. Bortz, F. Kondrashov, P.P. Łabaj, V. Romero, J. Hlávka, T.K. Oleksyk, S. Mangul, Science 378 (2022) 1285–1286.","ista":"Chhugani K, Frolova A, Salyha Y, Fiscutean A, Zlenko O, Reinsone S, Wolfsberger WW, Ivashchenko OV, Maci M, Dziuba D, Parkhomenko A, Bortz E, Kondrashov F, Łabaj PP, Romero V, Hlávka J, Oleksyk TK, Mangul S. 2022. Remote opportunities for scholars in Ukraine. Science. 378(6626), 1285–1286.","apa":"Chhugani, K., Frolova, A., Salyha, Y., Fiscutean, A., Zlenko, O., Reinsone, S., … Mangul, S. (2022). Remote opportunities for scholars in Ukraine. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adg0797\">https://doi.org/10.1126/science.adg0797</a>","ama":"Chhugani K, Frolova A, Salyha Y, et al. Remote opportunities for scholars in Ukraine. <i>Science</i>. 2022;378(6626):1285-1286. doi:<a href=\"https://doi.org/10.1126/science.adg0797\">10.1126/science.adg0797</a>","chicago":"Chhugani, Karishma, Alina Frolova, Yuriy Salyha, Andrada Fiscutean, Oksana Zlenko, Sanita Reinsone, Walter W. Wolfsberger, et al. “Remote Opportunities for Scholars in Ukraine.” <i>Science</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/science.adg0797\">https://doi.org/10.1126/science.adg0797</a>.","ieee":"K. Chhugani <i>et al.</i>, “Remote opportunities for scholars in Ukraine,” <i>Science</i>, vol. 378, no. 6626. American Association for the Advancement of Science, pp. 1285–1286, 2022."},"date_updated":"2023-10-03T11:01:06Z","abstract":[{"text":"Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure, including universities, research centers, and other academic infrastructure (1). Many Ukrainian scholars and researchers remain in Ukraine, and their work has suffered from major setbacks (2–4). We call on international scientists and institutions to support them.","lang":"eng"}],"day":"22","doi":"10.1126/science.adg0797","quality_controlled":"1","page":"1285-1286","article_type":"letter_note","publisher":"American Association for the Advancement of Science","issue":"6626","author":[{"first_name":"Karishma","last_name":"Chhugani","full_name":"Chhugani, Karishma"},{"last_name":"Frolova","first_name":"Alina","full_name":"Frolova, Alina"},{"first_name":"Yuriy","last_name":"Salyha","full_name":"Salyha, Yuriy"},{"first_name":"Andrada","last_name":"Fiscutean","full_name":"Fiscutean, Andrada"},{"first_name":"Oksana","last_name":"Zlenko","full_name":"Zlenko, Oksana"},{"full_name":"Reinsone, Sanita","last_name":"Reinsone","first_name":"Sanita"},{"first_name":"Walter W.","last_name":"Wolfsberger","full_name":"Wolfsberger, Walter W."},{"full_name":"Ivashchenko, Oleksandra V.","last_name":"Ivashchenko","first_name":"Oleksandra V."},{"last_name":"Maci","first_name":"Megi","full_name":"Maci, Megi"},{"first_name":"Dmytro","last_name":"Dziuba","full_name":"Dziuba, Dmytro"},{"full_name":"Parkhomenko, Andrii","last_name":"Parkhomenko","first_name":"Andrii"},{"full_name":"Bortz, Eric","first_name":"Eric","last_name":"Bortz"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Łabaj","first_name":"Paweł P.","full_name":"Łabaj, Paweł P."},{"last_name":"Romero","first_name":"Veronika","full_name":"Romero, Veronika"},{"full_name":"Hlávka, Jakub","first_name":"Jakub","last_name":"Hlávka"},{"first_name":"Taras K.","last_name":"Oleksyk","full_name":"Oleksyk, Taras K."},{"first_name":"Serghei","last_name":"Mangul","full_name":"Mangul, Serghei"}],"scopus_import":"1","_id":"12116","intvolume":"       378","title":"Remote opportunities for scholars in Ukraine","department":[{"_id":"FyKo"}],"article_processing_charge":"No","date_created":"2023-01-12T11:56:30Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"url":"https://doi.org/10.1126/science.adg0797","open_access":"1"}],"type":"journal_article","date_published":"2022-12-22T00:00:00Z","oa":1,"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"language":[{"iso":"eng"}],"publication":"Science","month":"12","oa_version":"Published Version"},{"article_type":"original","publisher":"Springer Nature","file_date_updated":"2021-08-16T11:36:49Z","quality_controlled":"1","ec_funded":1,"title":"Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains","intvolume":"        11","publication_status":"published","date_created":"2021-08-15T22:01:26Z","department":[{"_id":"FyKo"}],"article_processing_charge":"Yes","author":[{"full_name":"Rella, Simon","last_name":"Rella","first_name":"Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425"},{"full_name":"Kulikova, Yuliya A.","first_name":"Yuliya A.","last_name":"Kulikova"},{"first_name":"Emmanouil T.","last_name":"Dermitzakis","full_name":"Dermitzakis, Emmanouil T."},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"issue":"1","_id":"9905","pmid":1,"scopus_import":"1","ddc":["570","610"],"volume":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).","abstract":[{"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.","lang":"eng"}],"doi":"10.1038/s41598-021-95025-3","day":"30","isi":1,"external_id":{"pmid":["34330988"],"isi":["000683329100001"]},"date_updated":"2023-08-11T10:42:58Z","year":"2021","citation":{"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>.","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.","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>","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>","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.","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)."},"language":[{"iso":"eng"}],"month":"07","article_number":"15729","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209"}],"publication":"Scientific Reports","has_accepted_license":"1","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"url":"https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/","relation":"press_release","description":"News on IST Website"}]},"file":[{"date_created":"2021-08-16T11:36:49Z","checksum":"ac86892ed17e6724c7251844da5cef5c","file_size":3432001,"date_updated":"2021-08-16T11:36:49Z","file_name":"2021_ScientificReports_Rella.pdf","content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file","file_id":"9927","creator":"asandaue"}],"oa":1,"publication_identifier":{"eissn":["20452322"]},"date_published":"2021-07-30T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"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"}],"doi":"10.1038/s41431-021-00836-7","day":"01","isi":1,"external_id":{"pmid":["33664501"],"isi":["000625853200001"]},"date_updated":"2023-08-11T10:33:42Z","citation":{"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.","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>.","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.","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>","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.","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>."},"year":"2021","ddc":["576"],"volume":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).","title":"The limits of normal approximation for adult height","intvolume":"        29","publication_status":"published","department":[{"_id":"FyKo"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2021-08-15T22:01:28Z","author":[{"full_name":"Slavskii, Sergei A.","first_name":"Sergei A.","last_name":"Slavskii"},{"full_name":"Kuznetsov, Ivan A.","last_name":"Kuznetsov","first_name":"Ivan A."},{"full_name":"Shashkova, Tatiana I.","last_name":"Shashkova","first_name":"Tatiana I."},{"full_name":"Bazykin, Georgii A.","first_name":"Georgii A.","last_name":"Bazykin"},{"full_name":"Axenovich, Tatiana I.","last_name":"Axenovich","first_name":"Tatiana I."},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aulchenko, Yurii S.","first_name":"Yurii S.","last_name":"Aulchenko"}],"issue":"7","pmid":1,"_id":"9910","scopus_import":"1","article_type":"original","publisher":"Springer Nature","file_date_updated":"2021-08-16T09:14:36Z","page":"1082-1091","quality_controlled":"1","ec_funded":1,"oa":1,"publication_identifier":{"issn":["10184813"],"eissn":["14765438"]},"date_published":"2021-07-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_size":1079395,"checksum":"a676d76f91b0dbe0504c63e469129c2a","date_created":"2021-08-16T09:14:36Z","file_name":"2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf","content_type":"application/pdf","date_updated":"2021-08-16T09:14:36Z","success":1,"relation":"main_file","access_level":"open_access","creator":"asandaue","file_id":"9921"}],"month":"07","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"}],"publication":"European Journal of Human Genetics","has_accepted_license":"1","language":[{"iso":"eng"}]},{"pmid":1,"_id":"7889","scopus_import":"1","author":[{"first_name":"Tatiana","last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana"},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa","last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa"},{"last_name":"Markina","first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M."},{"last_name":"Chepurnyh","first_name":"Tatiana V.","full_name":"Chepurnyh, 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","first_name":"Kseniia A.","full_name":"Palkina, Kseniia A."},{"full_name":"Shakhova, Ekaterina S.","first_name":"Ekaterina S.","last_name":"Shakhova"},{"full_name":"Fakhranurova, Liliia I.","first_name":"Liliia I.","last_name":"Fakhranurova"},{"full_name":"Chekova, Sofia V.","first_name":"Sofia V.","last_name":"Chekova"},{"full_name":"Tsarkova, Aleksandra S.","first_name":"Aleksandra S.","last_name":"Tsarkova"},{"first_name":"Yaroslav V.","last_name":"Golubev","full_name":"Golubev, Yaroslav V."},{"full_name":"Negrebetsky, Vadim V.","last_name":"Negrebetsky","first_name":"Vadim V."},{"first_name":"Sergey A.","last_name":"Dolgushin","full_name":"Dolgushin, Sergey A."},{"last_name":"Shalaev","first_name":"Pavel V.","full_name":"Shalaev, Pavel V."},{"first_name":"Dmitry","last_name":"Shlykov","full_name":"Shlykov, Dmitry"},{"full_name":"Melnik, Olesya A.","last_name":"Melnik","first_name":"Olesya A."},{"full_name":"Shipunova, Victoria O.","first_name":"Victoria O.","last_name":"Shipunova"},{"last_name":"Deyev","first_name":"Sergey M.","full_name":"Deyev, Sergey M."},{"full_name":"Bubyrev, Andrey I.","first_name":"Andrey I.","last_name":"Bubyrev"},{"full_name":"Pushin, Alexander S.","last_name":"Pushin","first_name":"Alexander S."},{"full_name":"Choob, Vladimir V.","first_name":"Vladimir V.","last_name":"Choob"},{"last_name":"Dolgov","first_name":"Sergey V.","full_name":"Dolgov, Sergey V."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"},{"full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky","first_name":"Ilia V."},{"full_name":"Sarkisyan, Karen S.","first_name":"Karen S.","last_name":"Sarkisyan"}],"publication_status":"published","article_processing_charge":"No","date_created":"2020-05-25T15:02:00Z","department":[{"_id":"FyKo"}],"title":"Plants with genetically encoded autoluminescence","intvolume":"        38","page":"944-946","quality_controlled":"1","ec_funded":1,"file_date_updated":"2021-03-02T23:30:03Z","publisher":"Springer Nature","article_type":"original","date_updated":"2023-09-05T15:30:34Z","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>.","ieee":"T. Mitiouchkina <i>et al.</i>, “Plants with genetically encoded autoluminescence,” <i>Nature Biotechnology</i>, vol. 38. Springer Nature, pp. 944–946, 2020.","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>","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>","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.","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>."},"year":"2020","isi":1,"external_id":{"pmid":["32341562"],"isi":["000529298800003"]},"doi":"10.1038/s41587-020-0500-9","day":"27","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."}],"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,"ddc":["570"],"publication":"Nature Biotechnology","has_accepted_license":"1","oa_version":"Submitted Version","project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"month":"04","language":[{"iso":"eng"}],"date_published":"2020-04-27T00:00:00Z","type":"journal_article","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"oa":1,"file":[{"access_level":"open_access","relation":"main_file","file_id":"8316","creator":"dernst","embargo":"2021-03-01","date_created":"2020-08-28T08:57:07Z","checksum":"1b30467500ec6277229a875b06e196d0","file_size":1180086,"date_updated":"2021-03-02T23:30:03Z","content_type":"application/pdf","file_name":"2020_NatureBiotech_Mitiouchkina.pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","related_material":{"link":[{"url":"https://doi.org/10.1038/s41587-020-0578-0","relation":"erratum"}]}},{"ddc":["570"],"volume":10,"isi":1,"external_id":{"isi":["000560774200007"]},"date_updated":"2023-08-21T07:00:17Z","citation":{"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>.","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.","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>","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>","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.","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>."},"year":"2020","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."}],"doi":"10.1038/s41598-020-65406-1","day":"25","file_date_updated":"2020-07-14T12:48:05Z","quality_controlled":"1","article_type":"original","publisher":"Springer Nature","author":[{"first_name":"Leonid A.","last_name":"Uroshlev","full_name":"Uroshlev, Leonid A."},{"full_name":"Abdullaev, Eldar T.","first_name":"Eldar T.","last_name":"Abdullaev"},{"first_name":"Iren R.","last_name":"Umarova","full_name":"Umarova, Iren R."},{"full_name":"Il’Icheva, Irina A.","first_name":"Irina A.","last_name":"Il’Icheva"},{"last_name":"Panchenko","first_name":"Larisa A.","full_name":"Panchenko, Larisa A."},{"full_name":"Polozov, Robert V.","last_name":"Polozov","first_name":"Robert V."},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov"},{"first_name":"Yury D.","last_name":"Nechipurenko","full_name":"Nechipurenko, Yury D."},{"full_name":"Grokhovsky, Sergei L.","last_name":"Grokhovsky","first_name":"Sergei L."}],"_id":"7931","scopus_import":"1","title":"A method for identification of the methylation level of CpG islands from NGS data","intvolume":"        10","publication_status":"published","article_processing_charge":"No","date_created":"2020-06-07T22:00:51Z","department":[{"_id":"FyKo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","file":[{"checksum":"099e51611a5b7ca04244d03b2faddf33","file_size":1001724,"date_created":"2020-06-08T06:27:32Z","content_type":"application/pdf","file_name":"2020_ScientificReports_Uroshlev.pdf","date_updated":"2020-07-14T12:48:05Z","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"7947"}],"date_published":"2020-05-25T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["20452322"]},"language":[{"iso":"eng"}],"publication":"Scientific Reports","has_accepted_license":"1","month":"05","article_number":"8635","oa_version":"Published Version"},{"ddc":["510","530","570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","file":[{"file_id":"8152","creator":"dernst","relation":"main_file","access_level":"local","date_updated":"2020-07-22T14:45:07Z","file_name":"Core_Project_Proceedings_mod.pdf","content_type":"application/pdf","date_created":"2020-07-22T14:45:07Z","file_size":169620437}],"abstract":[{"lang":"eng","text":"The main idea behind the Core Project is to teach first year students at IST scientific communication skills and let them practice by presenting their research within an interdisciplinary environment. Over the course of the first semester, students participated in seminars, where they shared their results with the colleagues from other fields and took part in discussions on relevant subjects. The main focus during this sessions was on delivering the information in a simplified and comprehensible way, going into the very basics of a subject if necessary. At the end, the students were asked to present their research in the written form to exercise their writing skills. The reports were gathered in this document. All of them were reviewed by the  teaching assistants and write-ups illustrating unique stylistic features and, in general, an outstanding level of writing skills, were honorably mentioned in the section \"Selected Reports\"."}],"day":"01","type":"report","date_published":"2020-06-01T00:00:00Z","citation":{"apa":"Maslov, M., Kondrashov, F., Artner, C., Hennessey-Wesen, M., Kavcic, B., Machnik, N. N., … Tomanek, I. (2020). <i>Core Project Proceedings</i>. IST Austria.","ama":"Maslov M, Kondrashov F, Artner C, et al. <i>Core Project Proceedings</i>. IST Austria; 2020.","chicago":"Maslov, Mikhail, Fyodor Kondrashov, Christina Artner, Mike Hennessey-Wesen, Bor Kavcic, Nick N Machnik, Roshan K Satapathy, and Isabella Tomanek. <i>Core Project Proceedings</i>. IST Austria, 2020.","ieee":"M. Maslov <i>et al.</i>, <i>Core Project Proceedings</i>. IST Austria, 2020.","short":"M. Maslov, F. Kondrashov, C. Artner, M. Hennessey-Wesen, B. Kavcic, N.N. Machnik, R.K. Satapathy, I. Tomanek, Core Project Proceedings, IST Austria, 2020.","mla":"Maslov, Mikhail, et al. <i>Core Project Proceedings</i>. IST Austria, 2020.","ista":"Maslov M, Kondrashov F, Artner C, Hennessey-Wesen M, Kavcic B, Machnik NN, Satapathy RK, Tomanek I. 2020. Core Project Proceedings, IST Austria, 425p."},"year":"2020","date_updated":"2023-02-23T13:26:00Z","publisher":"IST Austria","language":[{"iso":"eng"}],"file_date_updated":"2020-07-22T14:45:07Z","page":"425","month":"06","title":"Core Project Proceedings","article_processing_charge":"No","date_created":"2020-07-22T14:48:14Z","publication_status":"published","oa_version":"None","author":[{"id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Maslov","orcid":"0000-0003-4074-2570","full_name":"Maslov, Mikhail"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Artner, Christina","first_name":"Christina","last_name":"Artner","id":"45DF286A-F248-11E8-B48F-1D18A9856A87"},{"id":"3F338C72-F248-11E8-B48F-1D18A9856A87","full_name":"Hennessey-Wesen, Mike","last_name":"Hennessey-Wesen","first_name":"Mike"},{"orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Machnik, Nick N","last_name":"Machnik","first_name":"Nick N","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87"},{"id":"46046B7A-F248-11E8-B48F-1D18A9856A87","last_name":"Satapathy","first_name":"Roshan K","full_name":"Satapathy, Roshan K"},{"id":"3981F020-F248-11E8-B48F-1D18A9856A87","last_name":"Tomanek","first_name":"Isabella","full_name":"Tomanek, Isabella","orcid":"0000-0001-6197-363X"}],"has_accepted_license":"1","_id":"8151"},{"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,"ddc":["000","570"],"day":"15","doi":"10.1093/bioinformatics/btz841","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"}],"year":"2020","citation":{"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.","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.","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 Academic, 2020, pp. 1960–62, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btz841\">10.1093/bioinformatics/btz841</a>.","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 Academic, 2020. <a href=\"https://doi.org/10.1093/bioinformatics/btz841\">https://doi.org/10.1093/bioinformatics/btz841</a>.","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 Academic, pp. 1960–1962, 2020.","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>","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 Academic. <a href=\"https://doi.org/10.1093/bioinformatics/btz841\">https://doi.org/10.1093/bioinformatics/btz841</a>"},"date_updated":"2023-08-22T09:57:29Z","external_id":{"isi":["000538696800054"],"pmid":["31742320"]},"isi":1,"publisher":"Oxford Academic","article_type":"original","quality_controlled":"1","ec_funded":1,"page":"1960-1962","file_date_updated":"2020-10-12T12:02:09Z","department":[{"_id":"FyKo"}],"date_created":"2020-10-11T22:01:14Z","article_processing_charge":"No","publication_status":"published","intvolume":"        36","title":"HypercubeME: Two hundred million combinatorially complete datasets from a single experiment","scopus_import":"1","pmid":1,"_id":"8645","issue":"6","author":[{"last_name":"Esteban","first_name":"Laura A","full_name":"Esteban, Laura A"},{"full_name":"Lonishin, Lyubov R","last_name":"Lonishin","first_name":"Lyubov R"},{"first_name":"Daniil M","last_name":"Bobrovskiy","full_name":"Bobrovskiy, Daniil M"},{"full_name":"Leleytner, Gregory","last_name":"Leleytner","first_name":"Gregory"},{"last_name":"Bogatyreva","first_name":"Natalya S","full_name":"Bogatyreva, Natalya S"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ivankov, Dmitry N ","first_name":"Dmitry N ","last_name":"Ivankov"}],"file":[{"file_id":"8649","creator":"dernst","relation":"main_file","success":1,"access_level":"open_access","date_updated":"2020-10-12T12:02:09Z","file_name":"2020_Bioinformatics_Esteban.pdf","content_type":"application/pdf","date_created":"2020-10-12T12:02:09Z","checksum":"21d6f71839deb3b83e4a356193f72767","file_size":308341}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1460-2059"],"issn":["1367-4803"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"type":"journal_article","date_published":"2020-03-15T00:00:00Z","language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution"}],"oa_version":"Published Version","month":"03","has_accepted_license":"1","publication":"Bioinformatics"},{"year":"2019","citation":{"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.","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>.","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.","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>","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>","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.","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>."},"date_updated":"2023-09-06T14:32:52Z","external_id":{"pmid":["31792410"],"isi":["000500748900021"]},"isi":1,"day":"01","doi":"10.1038/s41587-019-0333-6","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."}],"volume":37,"scopus_import":"1","pmid":1,"_id":"7181","issue":"12","author":[{"full_name":"Garriga, Edgar","first_name":"Edgar","last_name":"Garriga"},{"first_name":"Paolo","last_name":"Di Tommaso","full_name":"Di Tommaso, Paolo"},{"last_name":"Magis","first_name":"Cedrik","full_name":"Magis, Cedrik"},{"full_name":"Erb, Ionas","last_name":"Erb","first_name":"Ionas"},{"last_name":"Mansouri","first_name":"Leila","full_name":"Mansouri, Leila"},{"last_name":"Baltzis","first_name":"Athanasios","full_name":"Baltzis, Athanasios"},{"full_name":"Laayouni, Hafid","last_name":"Laayouni","first_name":"Hafid"},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"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","department":[{"_id":"FyKo"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        37","title":"Large multiple sequence alignments with a root-to-leaf regressive method","ec_funded":1,"quality_controlled":"1","page":"1466-1470","publisher":"Springer Nature","article_type":"original","type":"journal_article","date_published":"2019-12-01T00:00:00Z","publication_identifier":{"issn":["10870156"],"eissn":["15461696"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","related_material":{"record":[{"id":"13059","relation":"research_data","status":"public"}]},"publication":"Nature Biotechnology","project":[{"name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Submitted Version","month":"12","language":[{"iso":"eng"}]},{"volume":15,"ddc":["570"],"citation":{"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.","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).","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>.","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>.","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.","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>","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>"},"year":"2019","date_updated":"2023-08-25T10:30:37Z","external_id":{"isi":["000466866000029"]},"isi":1,"day":"10","doi":"10.1371/journal.pgen.1008079","abstract":[{"lang":"eng","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."}],"ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:47:30Z","publisher":"Public Library of Science","scopus_import":"1","_id":"6419","issue":"4","author":[{"first_name":"Victoria","last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Usmanova, Dinara R.","last_name":"Usmanova","first_name":"Dinara R."},{"first_name":"Ekaterina V.","last_name":"Putintseva","full_name":"Putintseva, Ekaterina V."},{"first_name":"Lorena","last_name":"Espinar","full_name":"Espinar, Lorena"},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341","last_name":"Sarkisyan","first_name":"Karen"},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"full_name":"Bogatyreva, Natalya S.","first_name":"Natalya S.","last_name":"Bogatyreva"},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","full_name":"Ivankov, Dmitry","first_name":"Dmitry","last_name":"Ivankov"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","first_name":"Arseniy"},{"full_name":"Avvakumov, Sergey","last_name":"Avvakumov","first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Povolotskaya","first_name":"Inna S.","full_name":"Povolotskaya, Inna S."},{"full_name":"Filion, Guillaume J.","first_name":"Guillaume J.","last_name":"Filion"},{"full_name":"Carey, Lucas B.","last_name":"Carey","first_name":"Lucas B."},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"FyKo"}],"article_processing_charge":"No","date_created":"2019-05-13T07:58:38Z","publication_status":"published","intvolume":"        15","title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","file":[{"file_id":"6445","creator":"dernst","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:30Z","content_type":"application/pdf","file_name":"2019_PLOSGenetics_Pokusaeva.pdf","date_created":"2019-05-14T08:26:08Z","checksum":"cf3889c8a8a16053dacf9c3776cbe217","file_size":3726017}],"status":"public","related_material":{"record":[{"status":"public","relation":"research_data","id":"9789"},{"status":"public","id":"9790","relation":"research_data"},{"id":"9797","relation":"research_data","status":"public"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2019-04-10T00:00:00Z","publication_identifier":{"eissn":["15537404"]},"oa":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"PLoS Genetics","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","article_number":"e1008079","month":"04"},{"citation":{"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. Multiple alignment of His3 orthologues, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1008079.s010\">10.1371/journal.pgen.1008079.s010</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, (2019).","mla":"Pokusaeva, Victoria, et al. <i>Multiple Alignment of His3 Orthologues</i>. Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079.s010\">10.1371/journal.pgen.1008079.s010</a>.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple Alignment of His3 Orthologues.” Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pgen.1008079.s010\">https://doi.org/10.1371/journal.pgen.1008079.s010</a>.","ieee":"V. Pokusaeva <i>et al.</i>, “Multiple alignment of His3 orthologues.” Public Library of Science, 2019.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1008079.s010\">https://doi.org/10.1371/journal.pgen.1008079.s010</a>","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. 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A statistical summary of segment libraries and sequencing results, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1008079.s011\">10.1371/journal.pgen.1008079.s011</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, (2019).","mla":"Pokusaeva, Victoria, et al. <i>A Statistical Summary of Segment Libraries and Sequencing Results</i>. Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079.s011\">10.1371/journal.pgen.1008079.s011</a>.","ieee":"V. Pokusaeva <i>et al.</i>, “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. 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