[{"quality_controlled":"1","isi":1,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000466866000029"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1008079","month":"04","publication_identifier":{"eissn":["15537404"]},"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Public Library of Science","year":"2019","date_created":"2019-05-13T07:58:38Z","date_updated":"2023-08-25T10:30:37Z","volume":15,"author":[{"orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","first_name":"Victoria","full_name":"Pokusaeva, Victoria"},{"first_name":"Dinara R.","last_name":"Usmanova","full_name":"Usmanova, Dinara R."},{"full_name":"Putintseva, Ekaterina V.","last_name":"Putintseva","first_name":"Ekaterina V."},{"first_name":"Lorena","last_name":"Espinar","full_name":"Espinar, Lorena"},{"full_name":"Sarkisyan, Karen","last_name":"Sarkisyan","first_name":"Karen","orcid":"0000-0002-5375-6341","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"full_name":"Bogatyreva, Natalya S.","first_name":"Natalya S.","last_name":"Bogatyreva"},{"full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","last_name":"Ivankov"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy"},{"id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","last_name":"Avvakumov","first_name":"Sergey","full_name":"Avvakumov, Sergey"},{"full_name":"Povolotskaya, Inna S.","first_name":"Inna S.","last_name":"Povolotskaya"},{"first_name":"Guillaume J.","last_name":"Filion","full_name":"Filion, Guillaume J."},{"full_name":"Carey, Lucas B.","first_name":"Lucas B.","last_name":"Carey"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"}],"related_material":{"record":[{"id":"9789","status":"public","relation":"research_data"},{"id":"9790","status":"public","relation":"research_data"},{"id":"9797","relation":"research_data","status":"public"}]},"article_number":"e1008079","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:30Z","ec_funded":1,"publication":"PLoS Genetics","citation":{"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. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079","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.","ieee":"V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, 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. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079","mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.","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).","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.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079."},"date_published":"2019-04-10T00:00:00Z","scopus_import":"1","day":"10","article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"status":"public","title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","intvolume":" 15","_id":"6419","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":3726017,"file_name":"2019_PLOSGenetics_Pokusaeva.pdf","access_level":"open_access","date_created":"2019-05-14T08:26:08Z","date_updated":"2020-07-14T12:47:30Z","checksum":"cf3889c8a8a16053dacf9c3776cbe217","file_id":"6445","relation":"main_file"}],"type":"journal_article","abstract":[{"text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible.","lang":"eng"}],"issue":"4"},{"citation":{"mla":"Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.","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).","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011","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. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011","ieee":"V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019."},"doi":"10.1371/journal.pgen.1008079.s011","date_published":"2019-04-10T00:00:00Z","day":"10","month":"04","article_processing_charge":"No","_id":"9790","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"A statistical summary of segment libraries and sequencing results","status":"public","department":[{"_id":"FyKo"}],"publisher":"Public Library of Science","author":[{"full_name":"Pokusaeva, Victoria","first_name":"Victoria","last_name":"Pokusaeva","id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X"},{"last_name":"Usmanova","first_name":"Dinara R.","full_name":"Usmanova, Dinara R."},{"full_name":"Putintseva, Ekaterina V.","last_name":"Putintseva","first_name":"Ekaterina V."},{"full_name":"Espinar, Lorena","first_name":"Lorena","last_name":"Espinar"},{"full_name":"Sarkisyan, Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5375-6341","first_name":"Karen","last_name":"Sarkisyan"},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"first_name":"Natalya S.","last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S."},{"last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","full_name":"Ivankov, Dmitry"},{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy"},{"last_name":"Avvakumov","first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey"},{"full_name":"Povolotskaya, Inna S.","first_name":"Inna S.","last_name":"Povolotskaya"},{"last_name":"Filion","first_name":"Guillaume J.","full_name":"Filion, Guillaume J."},{"last_name":"Carey","first_name":"Lucas B.","full_name":"Carey, Lucas B."},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"}],"related_material":{"record":[{"id":"6419","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-08-25T10:30:36Z","date_created":"2021-08-06T08:50:15Z","oa_version":"Published Version","type":"research_data_reference"},{"doi":"10.1371/journal.pgen.1008079.s011","date_published":"2019-04-10T00:00:00Z","citation":{"short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).","mla":"Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011","ieee":"V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011."},"article_processing_charge":"No","day":"10","month":"04","oa_version":"Published Version","date_created":"2021-08-06T11:08:20Z","date_updated":"2023-08-25T10:30:36Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6419"}]},"author":[{"full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X","first_name":"Victoria","last_name":"Pokusaeva"},{"full_name":"Usmanova, Dinara R.","last_name":"Usmanova","first_name":"Dinara R."},{"first_name":"Ekaterina V.","last_name":"Putintseva","full_name":"Putintseva, Ekaterina V."},{"full_name":"Espinar, Lorena","first_name":"Lorena","last_name":"Espinar"},{"full_name":"Sarkisyan, Karen","last_name":"Sarkisyan","first_name":"Karen","orcid":"0000-0002-5375-6341","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mishin, Alexander S.","first_name":"Alexander S.","last_name":"Mishin"},{"full_name":"Bogatyreva, Natalya S.","first_name":"Natalya S.","last_name":"Bogatyreva"},{"full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","last_name":"Ivankov","first_name":"Dmitry"},{"last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"first_name":"Inna S.","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S."},{"full_name":"Filion, Guillaume J.","first_name":"Guillaume J.","last_name":"Filion"},{"full_name":"Carey, Lucas B.","first_name":"Lucas B.","last_name":"Carey"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"}],"department":[{"_id":"FyKo"}],"publisher":"Public Library of Science","title":"A statistical summary of segment libraries and sequencing results","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9797","year":"2019","type":"research_data_reference"},{"title":"Multiple alignment of His3 orthologues","status":"public","publisher":"Public Library of Science","department":[{"_id":"FyKo"}],"_id":"9789","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-25T10:30:36Z","date_created":"2021-08-06T08:38:50Z","oa_version":"Published Version","author":[{"full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","id":"3184041C-F248-11E8-B48F-1D18A9856A87","last_name":"Pokusaeva","first_name":"Victoria"},{"last_name":"Usmanova","first_name":"Dinara R.","full_name":"Usmanova, Dinara R."},{"last_name":"Putintseva","first_name":"Ekaterina V.","full_name":"Putintseva, Ekaterina V."},{"full_name":"Espinar, Lorena","first_name":"Lorena","last_name":"Espinar"},{"full_name":"Sarkisyan, Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5375-6341","first_name":"Karen","last_name":"Sarkisyan"},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"last_name":"Bogatyreva","first_name":"Natalya S.","full_name":"Bogatyreva, Natalya S."},{"full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","last_name":"Ivankov"},{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"full_name":"Avvakumov, Sergey","first_name":"Sergey","last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Povolotskaya","first_name":"Inna S.","full_name":"Povolotskaya, Inna S."},{"first_name":"Guillaume J.","last_name":"Filion","full_name":"Filion, Guillaume J."},{"last_name":"Carey","first_name":"Lucas B.","full_name":"Carey, Lucas B."},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"}],"related_material":{"record":[{"id":"6419","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","citation":{"ieee":"V. Pokusaeva et al., “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. https://doi.org/10.1371/journal.pgen.1008079.s010","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, 10.1371/journal.pgen.1008079.s010.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3 orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010","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. https://doi.org/10.1371/journal.pgen.1008079.s010.","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. Multiple Alignment of His3 Orthologues. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010."},"doi":"10.1371/journal.pgen.1008079.s010","date_published":"2019-04-10T00:00:00Z","month":"04","day":"10","article_processing_charge":"No"},{"volume":10,"date_created":"2018-12-11T11:46:10Z","date_updated":"2023-09-11T13:56:52Z","author":[{"full_name":"Hönigschmid, Peter","first_name":"Peter","last_name":"Hönigschmid"},{"full_name":"Bykova, Nadya","last_name":"Bykova","first_name":"Nadya"},{"first_name":"René","last_name":"Schneider","full_name":"Schneider, René"},{"last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","full_name":"Ivankov, Dmitry"},{"full_name":"Frishman, Dmitrij","last_name":"Frishman","first_name":"Dmitrij"}],"publisher":"Oxford University Press","department":[{"_id":"FyKo"}],"publication_status":"published","acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft (grant number FR 1411/9-1). This work was supported by the German Research Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","year":"2018","publist_id":"7445","file_date_updated":"2020-07-14T12:46:16Z","language":[{"iso":"eng"}],"doi":"10.1093/gbe/evy049","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000429483700022"]},"month":"03","oa_version":"Published Version","file":[{"file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","access_level":"open_access","content_type":"application/pdf","file_size":691602,"creator":"system","relation":"main_file","file_id":"4667","date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-12T10:08:07Z","checksum":"458a7c2c2e79528567edfeb0f326cbe0"}],"pubrep_id":"999","intvolume":" 10","status":"public","ddc":["576"],"title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"384","issue":"3","abstract":[{"lang":"eng","text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification."}],"type":"journal_article","date_published":"2018-03-01T00:00:00Z","page":"928 - 938","citation":{"mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy049.","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938.","ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy049"},"publication":"Genome Biology and Evolution","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1"},{"type":"journal_article","issue":"21","abstract":[{"lang":"eng","text":"Motivation\r\nComputational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5995","intvolume":" 34","status":"public","ddc":["570"],"title":"Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation","file":[{"file_id":"5997","relation":"main_file","checksum":"7e0495153f44211479674601d7f6ee03","date_updated":"2020-07-14T12:47:15Z","date_created":"2019-02-14T13:00:55Z","access_level":"open_access","file_name":"2018_Oxford_Usmanova.pdf","creator":"kschuh","file_size":291969,"content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"ista":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658.","apa":"Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340","ieee":"D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.","ama":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340","chicago":"Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics. Oxford University Press , 2018. https://doi.org/10.1093/bioinformatics/bty340.","mla":"Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics, vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340.","short":"D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658."},"publication":"Bioinformatics","page":"3653-3658","date_published":"2018-11-01T00:00:00Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:15Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","pmid":1,"year":"2018","department":[{"_id":"FyKo"}],"publisher":"Oxford University Press ","publication_status":"published","author":[{"full_name":"Usmanova, Dinara R","last_name":"Usmanova","first_name":"Dinara R"},{"first_name":"Natalya S","last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S"},{"last_name":"Ariño Bernad","first_name":"Joan","full_name":"Ariño Bernad, Joan"},{"first_name":"Aleksandra A","last_name":"Eremina","full_name":"Eremina, Aleksandra A"},{"full_name":"Gorshkova, Anastasiya A","first_name":"Anastasiya A","last_name":"Gorshkova"},{"full_name":"Kanevskiy, German M","last_name":"Kanevskiy","first_name":"German M"},{"last_name":"Lonishin","first_name":"Lyubov R","full_name":"Lonishin, Lyubov R"},{"first_name":"Alexander V","last_name":"Meister","full_name":"Meister, Alexander V"},{"full_name":"Yakupova, Alisa G","first_name":"Alisa G","last_name":"Yakupova"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"full_name":"Ivankov, Dmitry","first_name":"Dmitry","last_name":"Ivankov","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"}],"volume":34,"date_created":"2019-02-14T12:48:00Z","date_updated":"2023-09-19T14:31:13Z","publication_identifier":{"issn":["1367-4803","1460-2059"]},"month":"11","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000450038900008"],"pmid":["29722803"]},"project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"doi":"10.1093/bioinformatics/bty340","language":[{"iso":"eng"}]}]