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Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808850.v1\">https://doi.org/10.6084/m9.figshare.9808850.v1</a>","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808850.v1\">10.6084/m9.figshare.9808850.v1</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808850.v1"}],"day":"12","publisher":"Springer Nature","oa_version":"Published Version","status":"public","department":[{"_id":"FyKo"}],"year":"2019","type":"research_data_reference","_id":"9897","abstract":[{"lang":"eng","text":"Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes. Only 374 genes with typical length and domain composition were considered. (CSV 6 kb)"}],"doi":"10.6084/m9.figshare.9808850.v1","author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","first_name":"Olga"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","last_name":"Akkuratov","first_name":"Evgeny E."},{"last_name":"Burskaia","first_name":"Valentina","full_name":"Burskaia, Valentina"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"date_published":"2019-09-12T00:00:00Z","article_processing_charge":"No","date_updated":"2026-04-03T09:39:41Z","month":"09","fulldoi":"https://doi.org/10.6084/m9.figshare.9808850.v1","related_material":{"record":[{"relation":"used_in_publication","id":"6898","status":"public"}]},"date_created":"2021-08-12T07:58:15Z","title":"Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction"},{"date_created":"2021-08-12T08:10:23Z","related_material":{"record":[{"relation":"used_in_publication","id":"6898","status":"public"}]},"fulldoi":"https://doi.org/10.6084/m9.figshare.9808859.v1","title":"Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","article_processing_charge":"No","month":"09","date_updated":"2026-04-03T09:39:41Z","doi":"10.6084/m9.figshare.9808859.v1","date_published":"2019-09-12T00:00:00Z","author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga","orcid":"0000-0003-1006-6639","last_name":"Bochkareva"},{"full_name":"Shelyakin, Pavel V.","first_name":"Pavel V.","last_name":"Shelyakin"},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"last_name":"Akkuratov","first_name":"Evgeny E.","full_name":"Akkuratov, Evgeny E."},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"_id":"9898","abstract":[{"text":"All polyN tracts of length 5 or more nucleotides in sequences of genes from OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts implemented in the RAST pipeline. (CSV 133 kb)","lang":"eng"}],"status":"public","department":[{"_id":"FyKo"}],"year":"2019","type":"research_data_reference","day":"12","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.9808859.v1","open_access":"1"}],"oa_version":"Published Version","publisher":"Springer Nature","citation":{"apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808859.v1\">https://doi.org/10.6084/m9.figshare.9808859.v1</a>","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808859.v1\">10.6084/m9.figshare.9808859.v1</a>.","mla":"Sigalova, Olga M., et al. <i>Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808859.v1\">10.6084/m9.figshare.9808859.v1</a>.","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808859.v1\">10.6084/m9.figshare.9808859.v1</a>","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9808859.v1\">https://doi.org/10.6084/m9.figshare.9808859.v1</a>."},"oa":1},{"publisher":"Springer Nature","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808865.v1"}],"day":"12","citation":{"apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808865.v1\">https://doi.org/10.6084/m9.figshare.9808865.v1</a>","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808865.v1\">10.6084/m9.figshare.9808865.v1</a>.","mla":"Sigalova, Olga M., et al. <i>Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808865.v1\">10.6084/m9.figshare.9808865.v1</a>.","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9808865.v1\">https://doi.org/10.6084/m9.figshare.9808865.v1</a>.","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808865.v1\">10.6084/m9.figshare.9808865.v1</a>"},"oa":1,"year":"2019","type":"research_data_reference","status":"public","department":[{"_id":"FyKo"}],"author":[{"last_name":"Sigalova","first_name":"Olga M.","full_name":"Sigalova, Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","first_name":"Olga"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","last_name":"Filaretov","first_name":"Vsevolod A."},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"date_published":"2019-09-12T00:00:00Z","doi":"10.6084/m9.figshare.9808865.v1","abstract":[{"lang":"eng","text":"Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb)"}],"_id":"9899","title":"Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","fulldoi":"https://doi.org/10.6084/m9.figshare.9808865.v1","related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"date_created":"2021-08-12T08:18:09Z","date_updated":"2026-04-03T09:39:41Z","month":"09","article_processing_charge":"No"},{"status":"public","department":[{"_id":"FyKo"}],"year":"2019","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808886.v1"}],"day":"12","publisher":"Springer Nature","oa_version":"Published Version","oa":1,"citation":{"short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">https://doi.org/10.6084/m9.figshare.9808886.v1</a>.","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">10.6084/m9.figshare.9808886.v1</a>","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","mla":"Sigalova, Olga M., et al. <i>Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">10.6084/m9.figshare.9808886.v1</a>.","ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">10.6084/m9.figshare.9808886.v1</a>.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808886.v1\">https://doi.org/10.6084/m9.figshare.9808886.v1</a>"},"fulldoi":"https://doi.org/10.6084/m9.figshare.9808886.v1","related_material":{"record":[{"relation":"used_in_publication","id":"6898","status":"public"}]},"date_created":"2021-08-12T08:44:49Z","title":"Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","article_processing_charge":"No","date_updated":"2026-04-03T09:39:41Z","month":"09","doi":"10.6084/m9.figshare.9808886.v1","author":[{"full_name":"Sigalova, Olga M.","first_name":"Olga M.","last_name":"Sigalova"},{"last_name":"Chaplin","first_name":"Andrei V.","full_name":"Chaplin, Andrei V."},{"first_name":"Olga","last_name":"Bochkareva","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"first_name":"Pavel V.","last_name":"Shelyakin","full_name":"Shelyakin, Pavel V."},{"full_name":"Filaretov, Vsevolod A.","first_name":"Vsevolod A.","last_name":"Filaretov"},{"full_name":"Akkuratov, Evgeny E.","first_name":"Evgeny E.","last_name":"Akkuratov"},{"first_name":"Valentina","last_name":"Burskaia","full_name":"Burskaia, Valentina"},{"full_name":"Gelfand, Mikhail S.","last_name":"Gelfand","first_name":"Mikhail S."}],"date_published":"2019-09-12T00:00:00Z","_id":"9900","abstract":[{"text":"Pan-genome statistics by species. (CSV 3 kb)","lang":"eng"}]},{"doi":"10.6084/m9.figshare.9808907.v1","date_published":"2019-09-12T00:00:00Z","author":[{"full_name":"Sigalova, Olga M.","last_name":"Sigalova","first_name":"Olga M."},{"first_name":"Andrei V.","last_name":"Chaplin","full_name":"Chaplin, Andrei V."},{"last_name":"Bochkareva","orcid":"0000-0003-1006-6639","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga"},{"full_name":"Shelyakin, Pavel V.","first_name":"Pavel V.","last_name":"Shelyakin"},{"first_name":"Vsevolod A.","last_name":"Filaretov","full_name":"Filaretov, Vsevolod A."},{"first_name":"Evgeny E.","last_name":"Akkuratov","full_name":"Akkuratov, Evgeny E."},{"full_name":"Burskaia, Valentina","first_name":"Valentina","last_name":"Burskaia"},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"_id":"9901","abstract":[{"lang":"eng","text":"Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb)"}],"related_material":{"record":[{"id":"6898","relation":"used_in_publication","status":"public"}]},"date_created":"2021-08-12T10:54:03Z","fulldoi":"https://doi.org/10.6084/m9.figshare.9808907.v1","title":"Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction","article_processing_charge":"No","date_updated":"2026-04-03T09:39:41Z","month":"09","day":"12","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.9808907.v1"}],"oa_version":"Published Version","publisher":"Springer Nature","citation":{"ista":"Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">10.6084/m9.figshare.9808907.v1</a>.","apa":"Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">https://doi.org/10.6084/m9.figshare.9808907.v1</a>","short":"O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).","ama":"Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">10.6084/m9.figshare.9808907.v1</a>","chicago":"Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. <a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">https://doi.org/10.6084/m9.figshare.9808907.v1</a>.","ieee":"O. M. Sigalova <i>et al.</i>, “Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019.","mla":"Sigalova, Olga M., et al. <i>Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>. Springer Nature, 2019, doi:<a href=\"https://doi.org/10.6084/m9.figshare.9808907.v1\">10.6084/m9.figshare.9808907.v1</a>."},"oa":1,"department":[{"_id":"FyKo"}],"status":"public","type":"research_data_reference","year":"2019"},{"isi":1,"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"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1553-7404"]},"doi":"10.1371/journal.pgen.1008079","ddc":["570"],"volume":15,"intvolume":"        15","fulldoi":"https://doi.org/10.1371/journal.pgen.1008079","related_material":{"record":[{"relation":"research_data","id":"9789","status":"public"},{"status":"public","relation":"research_data","id":"9790"},{"status":"public","id":"9797","relation":"research_data"}]},"citation":{"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>.","ama":"Pokusaeva V, Usmanova DR, Putintseva E, 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>","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina 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>.","short":"V. Pokusaeva, D.R. Usmanova, E. 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).","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., 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>","ista":"Pokusaeva V, Usmanova DR, Putintseva E, 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."},"issue":"4","external_id":{"isi":["000466866000029"]},"oa_version":"Published Version","day":"10","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1","_id":"6419","ec_funded":1,"author":[{"first_name":"Victoria","orcid":"0000-0001-7660-444X","last_name":"Pokusaeva","full_name":"Pokusaeva, Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Usmanova, Dinara R.","last_name":"Usmanova","first_name":"Dinara R."},{"last_name":"Putintseva","first_name":"Ekaterina","id":"2EF67C84-F248-11E8-B48F-1D18A9856A87","full_name":"Putintseva, Ekaterina"},{"full_name":"Espinar, Lorena","first_name":"Lorena","last_name":"Espinar"},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","full_name":"Sarkisyan, Karen","last_name":"Sarkisyan","orcid":"0000-0002-5375-6341","first_name":"Karen"},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"first_name":"Natalya S.","last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S."},{"full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","last_name":"Ivankov","orcid":"0000-0002-8224-4118"},{"first_name":"Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey","orcid":"0000-0002-7840-5062","last_name":"Avvakumov"},{"first_name":"Inna S.","last_name":"Povolotskaya","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."},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2019-04-10T00:00:00Z","publication":"PLoS Genetics","file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"2019_PLOSGenetics_Pokusaeva.pdf","creator":"dernst","checksum":"cf3889c8a8a16053dacf9c3776cbe217","relation":"main_file","date_updated":"2020-07-14T12:47:30Z","file_id":"6445","file_size":3726017,"date_created":"2019-05-14T08:26:08Z"}],"month":"04","date_updated":"2026-07-28T13:29:02Z","article_processing_charge":"No","title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","date_created":"2019-05-13T07:58:38Z","article_number":"e1008079","quality_controlled":"1","oa":1,"publisher":"Public Library of Science","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:30Z","type":"journal_article","year":"2019","scopus_import":"1","department":[{"_id":"FyKo"}],"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}]},{"citation":{"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. <a href=\"https://doi.org/10.1371/journal.pgen.1008079.s011\">https://doi.org/10.1371/journal.pgen.1008079.s011</a>.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 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.","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>.","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, <a href=\"https://doi.org/10.1371/journal.pgen.1008079.s011\">10.1371/journal.pgen.1008079.s011</a>.","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. <a href=\"https://doi.org/10.1371/journal.pgen.1008079.s011\">https://doi.org/10.1371/journal.pgen.1008079.s011</a>"},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"10","publisher":"Public Library of Science","oa_version":"Published Version","status":"public","department":[{"_id":"FyKo"}],"year":"2019","type":"research_data_reference","_id":"9790","doi":"10.1371/journal.pgen.1008079.s011","author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","full_name":"Pokusaeva, Victoria","orcid":"0000-0001-7660-444X","last_name":"Pokusaeva","first_name":"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."},{"full_name":"Espinar, Lorena","first_name":"Lorena","last_name":"Espinar"},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","full_name":"Sarkisyan, Karen","last_name":"Sarkisyan","orcid":"0000-0002-5375-6341","first_name":"Karen"},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"first_name":"Natalya S.","last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S."},{"orcid":"0000-0002-8224-4118","last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","full_name":"Ivankov, Dmitry"},{"first_name":"Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sergey","orcid":"0000-0002-7840-5062","last_name":"Avvakumov","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya","first_name":"Inna S."},{"full_name":"Filion, Guillaume J.","first_name":"Guillaume J.","last_name":"Filion"},{"first_name":"Lucas B.","last_name":"Carey","full_name":"Carey, Lucas B."},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2019-04-10T00:00:00Z","article_processing_charge":"No","month":"04","date_updated":"2026-07-28T13:29:02Z","fulldoi":"https://doi.org/10.1371/journal.pgen.1008079.s011","related_material":{"record":[{"relation":"used_in_publication","id":"6419","status":"public"}]},"date_created":"2021-08-06T08:50:15Z","title":"A statistical summary of segment libraries and sequencing results"},{"doi":"10.1371/journal.pgen.1008079.s011","author":[{"last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","full_name":"Pokusaeva, Victoria"},{"full_name":"Usmanova, Dinara R.","last_name":"Usmanova","first_name":"Dinara R."},{"full_name":"Putintseva, Ekaterina V.","last_name":"Putintseva","first_name":"Ekaterina V."},{"full_name":"Espinar, Lorena","last_name":"Espinar","first_name":"Lorena"},{"orcid":"0000-0002-5375-6341","last_name":"Sarkisyan","first_name":"Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","full_name":"Sarkisyan, Karen"},{"full_name":"Mishin, Alexander S.","first_name":"Alexander S.","last_name":"Mishin"},{"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","orcid":"0000-0002-8224-4118"},{"full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X"},{"full_name":"Povolotskaya, Inna S.","first_name":"Inna S.","last_name":"Povolotskaya"},{"full_name":"Filion, Guillaume J.","last_name":"Filion","first_name":"Guillaume J."},{"full_name":"Carey, Lucas B.","last_name":"Carey","first_name":"Lucas B."},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2019-04-10T00:00:00Z","_id":"9797","fulldoi":"https://doi.org/10.1371/journal.pgen.1008079.s011","date_created":"2021-08-06T11:08:20Z","related_material":{"record":[{"status":"public","id":"6419","relation":"used_in_publication"}]},"title":"A statistical summary of segment libraries and sequencing results","article_processing_charge":"No","date_updated":"2026-07-28T13:29:02Z","month":"04","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"10","publisher":"Public Library of Science","oa_version":"Published Version","citation":{"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, <a href=\"https://doi.org/10.1371/journal.pgen.1008079.s011\">10.1371/journal.pgen.1008079.s011</a>.","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. <a href=\"https://doi.org/10.1371/journal.pgen.1008079.s011\">https://doi.org/10.1371/journal.pgen.1008079.s011</a>","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079.s011\">10.1371/journal.pgen.1008079.s011</a>","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. <a href=\"https://doi.org/10.1371/journal.pgen.1008079.s011\">https://doi.org/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, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019).","ieee":"V. Pokusaeva <i>et al.</i>, “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 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>."},"department":[{"_id":"FyKo"}],"status":"public","year":"2019","type":"research_data_reference"},{"month":"04","date_updated":"2026-07-28T13:29:01Z","article_processing_charge":"No","title":"Multiple alignment of His3 orthologues","date_created":"2021-08-06T08:38:50Z","related_material":{"record":[{"relation":"used_in_publication","id":"6419","status":"public"}]},"fulldoi":"https://doi.org/10.1371/journal.pgen.1008079.s010","_id":"9789","date_published":"2019-04-10T00:00:00Z","author":[{"last_name":"Pokusaeva","orcid":"0000-0001-7660-444X","first_name":"Victoria","id":"3184041C-F248-11E8-B48F-1D18A9856A87","full_name":"Pokusaeva, Victoria"},{"full_name":"Usmanova, Dinara R.","first_name":"Dinara R.","last_name":"Usmanova"},{"first_name":"Ekaterina V.","last_name":"Putintseva","full_name":"Putintseva, Ekaterina V."},{"last_name":"Espinar","first_name":"Lorena","full_name":"Espinar, Lorena"},{"full_name":"Sarkisyan, Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","orcid":"0000-0002-5375-6341","last_name":"Sarkisyan"},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"full_name":"Bogatyreva, Natalya S.","last_name":"Bogatyreva","first_name":"Natalya S."},{"id":"49FF1036-F248-11E8-B48F-1D18A9856A87","full_name":"Ivankov, Dmitry","last_name":"Ivankov","orcid":"0000-0002-8224-4118","first_name":"Dmitry"},{"first_name":"Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sergey","last_name":"Avvakumov","orcid":"0000-0002-7840-5062","full_name":"Avvakumov, 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.","first_name":"Lucas B.","last_name":"Carey"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor"}],"doi":"10.1371/journal.pgen.1008079.s010","type":"research_data_reference","year":"2019","department":[{"_id":"FyKo"}],"status":"public","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>.","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>","ieee":"V. Pokusaeva <i>et al.</i>, “Multiple alignment of His3 orthologues.” Public Library of Science, 2019.","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>.","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).","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3 orthologues. 2019. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079.s010\">10.1371/journal.pgen.1008079.s010</a>","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>."},"oa_version":"Published Version","publisher":"Public Library of Science","day":"10","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"volume":19,"ddc":["570"],"fulldoi":"https://doi.org/10.1186/s13059-018-1434-0","related_material":{"record":[{"relation":"research_data","id":"9811","status":"public"},{"status":"public","relation":"research_data","id":"9812"}]},"intvolume":"        19","language":[{"iso":"eng"}],"isi":1,"abstract":[{"lang":"eng","text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments."}],"doi":"10.1186/s13059-018-1434-0","has_accepted_license":"1","status":"public","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” <i>Genome Biology</i>, vol. 19. BioMed Central, 2018.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>, vol. 19, 67, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>"},"day":"31","external_id":{"isi":["000433986200001"]},"oa_version":"Published Version","article_processing_charge":"No","publist_id":"7620","date_updated":"2025-04-15T08:30:30Z","month":"05","date_created":"2018-12-11T11:45:35Z","title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","_id":"279","ec_funded":1,"publication":"Genome Biology","file":[{"file_size":1414722,"date_created":"2018-12-17T14:05:01Z","file_id":"5708","date_updated":"2020-07-14T12:45:47Z","file_name":"2018_GenomeBiology_Zapata.pdf","creator":"dernst","checksum":"f3e4922486bd9bf1483271bdbed394a7","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"full_name":"Serrano, Luis","first_name":"Luis","last_name":"Serrano"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ossowski, Stephan","last_name":"Ossowski","first_name":"Stephan"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"date_published":"2018-05-31T00:00:00Z","department":[{"_id":"FyKo"}],"project":[{"grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425","name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7"}],"type":"journal_article","scopus_import":"1","year":"2018","quality_controlled":"1","oa":1,"article_number":"67","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:45:47Z","publisher":"BioMed Central","publication_status":"published"},{"article_processing_charge":"No","date_updated":"2025-07-10T11:54:19Z","month":"12","ddc":["570"],"fulldoi":"https://doi.org/10.5281/ZENODO.2025846","date_created":"2023-05-23T16:08:20Z","related_material":{"record":[{"id":"7181","relation":"used_in_publication","status":"public"}]},"title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","_id":"13059","abstract":[{"lang":"eng","text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee)."}],"doi":"10.5281/ZENODO.2025846","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"},{"full_name":"Baltzis, Athanasios","first_name":"Athanasios","last_name":"Baltzis"},{"last_name":"Laayouni","first_name":"Hafid","full_name":"Laayouni, Hafid"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor"},{"full_name":"Floden, Evan","first_name":"Evan","last_name":"Floden"},{"first_name":"Cedric","last_name":"Notredame","full_name":"Notredame, Cedric"}],"date_published":"2018-12-07T00:00:00Z","status":"public","department":[{"_id":"FyKo"}],"year":"2018","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"research_data_reference","oa":1,"citation":{"mla":"Garriga, Edgar, et al. <i>Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","ieee":"E. Garriga <i>et al.</i>, “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>.","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>","ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3271452"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"07","publisher":"Zenodo","oa_version":"Published Version"},{"has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"issue":"50","citation":{"ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(50):12728-12732. doi:<a href=\"https://doi.org/10.1073/pnas.1803615115\">10.1073/pnas.1803615115</a>","short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.","chicago":"Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1803615115\">https://doi.org/10.1073/pnas.1803615115</a>.","ieee":"A. A. Kotlobay <i>et al.</i>, “Genetically encodable bioluminescent system from fungi,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018.","mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:<a href=\"https://doi.org/10.1073/pnas.1803615115\">10.1073/pnas.1803615115</a>.","ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.","apa":"Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1803615115\">https://doi.org/10.1073/pnas.1803615115</a>"},"day":"11","external_id":{"isi":["000452866000068"]},"oa_version":"Published Version","volume":115,"ddc":["580"],"fulldoi":"https://doi.org/10.1073/pnas.1803615115","intvolume":"       115","language":[{"iso":"eng"}],"isi":1,"abstract":[{"lang":"eng","text":"Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering."}],"doi":"10.1073/pnas.1803615115","publication_identifier":{"issn":["0027-8424"]},"department":[{"_id":"FyKo"}],"scopus_import":"1","year":"2018","type":"journal_article","oa":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"12728-12732","file_date_updated":"2020-07-14T12:47:11Z","publisher":"National Academy of Sciences","publication_status":"published","article_processing_charge":"No","date_updated":"2025-07-10T11:52:58Z","month":"12","date_created":"2018-12-23T22:59:18Z","title":"Genetically encodable bioluminescent system from fungi","_id":"5780","file":[{"date_updated":"2020-07-14T12:47:11Z","file_id":"5926","file_size":1271988,"date_created":"2019-02-05T15:21:40Z","access_level":"open_access","content_type":"application/pdf","file_name":"2018_PNAS_Kotlobay.pdf","creator":"dernst","relation":"main_file","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","author":[{"first_name":"Alexey A.","last_name":"Kotlobay","full_name":"Kotlobay, Alexey A."},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341","last_name":"Sarkisyan","first_name":"Karen"},{"first_name":"Yuliana A.","last_name":"Mokrushina","full_name":"Mokrushina, Yuliana A."},{"full_name":"Marcet-Houben, Marina","first_name":"Marina","last_name":"Marcet-Houben"},{"full_name":"Serebrovskaya, Ekaterina O.","first_name":"Ekaterina O.","last_name":"Serebrovskaya"},{"last_name":"Markina","first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M."},{"full_name":"Gonzalez Somermeyer, Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","first_name":"Louisa","orcid":"0000-0001-9139-5383","last_name":"Gonzalez Somermeyer"},{"full_name":"Gorokhovatsky, Andrey Y.","last_name":"Gorokhovatsky","first_name":"Andrey Y."},{"full_name":"Vvedensky, Andrey","first_name":"Andrey","last_name":"Vvedensky"},{"last_name":"Purtov","first_name":"Konstantin V.","full_name":"Purtov, Konstantin V."},{"first_name":"Valentin N.","last_name":"Petushkov","full_name":"Petushkov, Valentin N."},{"first_name":"Natalja S.","last_name":"Rodionova","full_name":"Rodionova, Natalja S."},{"first_name":"Tatiana V.","last_name":"Chepurnyh","full_name":"Chepurnyh, Tatiana V."},{"full_name":"Fakhranurova, Liliia","first_name":"Liliia","last_name":"Fakhranurova"},{"full_name":"Guglya, Elena B.","last_name":"Guglya","first_name":"Elena B."},{"full_name":"Ziganshin, Rustam","first_name":"Rustam","last_name":"Ziganshin"},{"first_name":"Aleksandra S.","last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S."},{"full_name":"Kaskova, Zinaida M.","last_name":"Kaskova","first_name":"Zinaida M."},{"full_name":"Shender, Victoria","first_name":"Victoria","last_name":"Shender"},{"full_name":"Abakumov, Maxim","first_name":"Maxim","last_name":"Abakumov"},{"first_name":"Tatiana O.","last_name":"Abakumova","full_name":"Abakumova, Tatiana O."},{"first_name":"Inna S.","last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S."},{"full_name":"Eroshkin, Fedor M.","first_name":"Fedor M.","last_name":"Eroshkin"},{"last_name":"Zaraisky","first_name":"Andrey G.","full_name":"Zaraisky, Andrey G."},{"full_name":"Mishin, Alexander S.","first_name":"Alexander S.","last_name":"Mishin"},{"first_name":"Sergey V.","last_name":"Dolgov","full_name":"Dolgov, Sergey V."},{"full_name":"Mitiouchkina, Tatiana Y.","first_name":"Tatiana Y.","last_name":"Mitiouchkina"},{"last_name":"Kopantzev","first_name":"Eugene P.","full_name":"Kopantzev, Eugene P."},{"last_name":"Waldenmaier","first_name":"Hans E.","full_name":"Waldenmaier, Hans E."},{"last_name":"Oliveira","first_name":"Anderson G.","full_name":"Oliveira, Anderson G."},{"last_name":"Oba","first_name":"Yuichi","full_name":"Oba, Yuichi"},{"full_name":"Barsova, Ekaterina","first_name":"Ekaterina","last_name":"Barsova"},{"full_name":"Bogdanova, Ekaterina A.","first_name":"Ekaterina A.","last_name":"Bogdanova"},{"full_name":"Gabaldón, Toni","first_name":"Toni","last_name":"Gabaldón"},{"first_name":"Cassius V.","last_name":"Stevani","full_name":"Stevani, Cassius V."},{"last_name":"Lukyanov","first_name":"Sergey","full_name":"Lukyanov, Sergey"},{"last_name":"Smirnov","first_name":"Ivan V.","full_name":"Smirnov, Ivan V."},{"full_name":"Gitelson, Josef I.","first_name":"Josef I.","last_name":"Gitelson"},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky","first_name":"Ilia V."}],"date_published":"2018-12-11T00:00:00Z"},{"title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","date_created":"2021-08-06T12:53:49Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"279"}]},"fulldoi":"https://doi.org/10.6084/m9.figshare.6401390.v1","month":"05","date_updated":"2025-04-15T08:30:30Z","article_processing_charge":"No","date_published":"2018-05-31T00:00:00Z","author":[{"last_name":"Zapata","first_name":"Luis","full_name":"Zapata, Luis"},{"full_name":"Pich, Oriol","first_name":"Oriol","last_name":"Pich"},{"first_name":"Luis","last_name":"Serrano","full_name":"Serrano, Luis"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ossowski, Stephan","last_name":"Ossowski","first_name":"Stephan"},{"last_name":"Schaefer","first_name":"Martin","full_name":"Schaefer, Martin"}],"doi":"10.6084/m9.figshare.6401390.v1","abstract":[{"text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)","lang":"eng"}],"_id":"9811","type":"research_data_reference","year":"2018","status":"public","department":[{"_id":"FyKo"}],"oa_version":"Preprint","publisher":"Springer Nature","day":"31","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401390.v1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"citation":{"mla":"Zapata, Luis, et al. <i>Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>.","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">https://doi.org/10.6084/m9.figshare.6401390.v1</a>.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">https://doi.org/10.6084/m9.figshare.6401390.v1</a>","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>."}},{"article_processing_charge":"No","date_updated":"2025-04-15T08:30:30Z","month":"05","date_created":"2021-08-06T12:58:25Z","related_material":{"record":[{"status":"public","id":"279","relation":"used_in_publication"}]},"fulldoi":"https://doi.org/10.6084/m9.figshare.6401414.v1","title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","_id":"9812","abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"doi":"10.6084/m9.figshare.6401414.v1","date_published":"2018-05-31T00:00:00Z","author":[{"first_name":"Luis","last_name":"Zapata","full_name":"Zapata, Luis"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"full_name":"Serrano, Luis","last_name":"Serrano","first_name":"Luis"},{"first_name":"Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ossowski","first_name":"Stephan","full_name":"Ossowski, Stephan"},{"last_name":"Schaefer","first_name":"Martin","full_name":"Schaefer, Martin"}],"department":[{"_id":"FyKo"}],"status":"public","type":"research_data_reference","year":"2018","oa":1,"citation":{"short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">https://doi.org/10.6084/m9.figshare.6401414.v1</a>.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","mla":"Zapata, Luis, et al. <i>Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">https://doi.org/10.6084/m9.figshare.6401414.v1</a>"},"day":"31","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401414.v1","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","publisher":"Springer Nature"},{"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","status":"public","oa_version":"Published Version","external_id":{"isi":["000429483700022"]},"day":"01","citation":{"apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., &#38; Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evy049\">https://doi.org/10.1093/gbe/evy049</a>","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.","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” <i>Genome Biology and Evolution</i>, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:<a href=\"https://doi.org/10.1093/gbe/evy049\">10.1093/gbe/evy049</a>.","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. <i>Genome Biology and Evolution</i>. 2018;10(3):928-938. doi:<a href=\"https://doi.org/10.1093/gbe/evy049\">10.1093/gbe/evy049</a>","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.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/gbe/evy049\">https://doi.org/10.1093/gbe/evy049</a>.","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,” <i>Genome Biology and Evolution</i>, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018."},"issue":"3","intvolume":"        10","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","fulldoi":"https://doi.org/10.1093/gbe/evy049","ddc":["576"],"volume":10,"doi":"10.1093/gbe/evy049","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."}],"isi":1,"language":[{"iso":"eng"}],"type":"journal_article","year":"2018","scopus_import":"1","department":[{"_id":"FyKo"}],"publication_status":"published","publisher":"Oxford University Press","file_date_updated":"2020-07-14T12:46:16Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"928 - 938","oa":1,"quality_controlled":"1","title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","date_created":"2018-12-11T11:46:10Z","date_updated":"2023-09-11T13:56:52Z","month":"03","publist_id":"7445","article_processing_charge":"No","date_published":"2018-03-01T00:00:00Z","author":[{"first_name":"Peter","last_name":"Hönigschmid","full_name":"Hönigschmid, Peter"},{"full_name":"Bykova, Nadya","last_name":"Bykova","first_name":"Nadya"},{"first_name":"René","last_name":"Schneider","full_name":"Schneider, René"},{"first_name":"Dmitry","last_name":"Ivankov","full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Frishman, Dmitrij","last_name":"Frishman","first_name":"Dmitrij"}],"pubrep_id":"999","file":[{"date_updated":"2020-07-14T12:46:16Z","file_id":"4667","date_created":"2018-12-12T10:08:07Z","file_size":691602,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"458a7c2c2e79528567edfeb0f326cbe0","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","creator":"system"}],"publication":"Genome Biology and Evolution","_id":"384"}]