Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina, N. M., Gonzalez Somermeyer, L.,https://doi.org/10.1126/sciadv.adk1992__Sarkisyan, K. S. (2024). A hybrid pathway for self-sustained luminescence. Science Advances. American Association for the Advancement of Science.https://doi.org/10.1126/sciadv.adk1992 

Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E.,https://doi.org/10.1371/journal.pone.0282689__Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science.https://doi.org/10.1371/journal.pone.0282689 

Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L.,https://doi.org/10.1038/s41467-023-39317-4__Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. Springer Nature.https://doi.org/10.1038/s41467-023-39317-4 

Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko, O.,https://doi.org/10.1093/gigascience/giad045__Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine. GigaScience. Oxford Academic.https://doi.org/10.1093/gigascience/giad045 

Yurtseven, A., Buyanova, S., Agrawal, A. A. A., Bochkareva, O., &; Kalinina, O. V. V. (2023). Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. Springer Nature.https://doi.org/10.1186/s12866-023-03147-7 

Zabelkin, A., Yakovleva, Y., Bochkareva, O., &; Alexeev, N. (2022). PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. Oxford Academic.https://doi.org/10.1093/bioinformatics/btab691 

Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan, S.,https://doi.org/10.1038/s41592-022-01444-z__Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. Springer Nature.https://doi.org/10.1038/s41592-022-01444-z 

Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., &; Bochkareva, O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. Springer Nature.https://doi.org/10.1038/s41598-022-10827-3 

Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J.,https://doi.org/10.7554/elife.75842__Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. ELife. eLife Sciences Publications.https://doi.org/10.7554/elife.75842 

Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W.,https://doi.org/10.1186/s13059-022-02711-0__Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. BioMed Central.https://doi.org/10.1186/s13059-022-02711-0 

Byazrova, M. G., Astakhova, E. A., Minnegalieva, A., Sukhova, M. M., Mikhailov, A. A., Prilipov, A. G.,https://doi.org/10.1038/s41541-022-00566-x__Filatov, A. V. (2022). Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. Npj Vaccines. Springer Nature.https://doi.org/10.1038/s41541-022-00566-x 

Baumgartner, M., Zirnbauer, R., Schlager, S., Mertens, D., Gasche, N., Sladek, B.,https://doi.org/10.1080/19490976.2022.2143218__Gasche, C. (2022). Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis. Gut Microbes. Taylor &; Francis.https://doi.org/10.1080/19490976.2022.2143218 

Chhugani, K., Frolova, A., Salyha, Y., Fiscutean, A., Zlenko, O., Reinsone, S.,https://doi.org/10.1126/science.adg0797__Mangul, S. (2022). Remote opportunities for scholars in Ukraine. Science. American Association for the Advancement of Science.https://doi.org/10.1126/science.adg0797 

Pivoluska, M., Plesch, M., Farkas, M., Ruzickova, N., Flegel, C., Valencia, N. H.,https://doi.org/10.1038/s41534-021-00387-1__Aguilar, E. A. (2021). Semi-device-independent random number generation with flexible assumptions. Npj Quantum Information. Springer Nature.https://doi.org/10.1038/s41534-021-00387-1 

Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O., Alexeev, N.,https://doi.org/10.3389/fmicb.2021.628622__Bochkareva, O. (2021). High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. Frontiers.https://doi.org/10.3389/fmicb.2021.628622 

Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich, T. I., Kondrashov, F., &; Aulchenko, Y. S. (2021). The limits of normal approximation for adult height. European Journal of Human Genetics. Springer Nature.https://doi.org/10.1038/s41431-021-00836-7 

Rella, S., Kulikova, Y. A., Dermitzakis, E. T., &; Kondrashov, F. (2021). Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. Springer Nature.https://doi.org/10.1038/s41598-021-95025-3 

Nimeth, B. A., Riegler, S., &; Kalyna, M. (2020). Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. Frontiers.https://doi.org/10.3389/fpls.2020.00091 

Plesch, M., Plesník, S., &; Ruzickova, N. (2020). The IYPT and the “Ring Oiler”https://doi.org/10.1088/1361-6404/ab6414__problem. European Journal of Physics. IOP Publishing.https://doi.org/10.1088/1361-6404/ab6414 

Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V.,https://doi.org/10.1038/s41598-020-65406-1__Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. Springer Nature.https://doi.org/10.1038/s41598-020-65406-1 

Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., &; Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. Springer Nature.https://doi.org/10.1134/S0026893320040111 

Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V., &; Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences.https://doi.org/10.31857/S0026898420040126 

Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva, N. S., Kondrashov, F., &; Ivankov, D. N. (2020). HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. Oxford Academic.https://doi.org/10.1093/bioinformatics/btz841 

Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., &; Vaquerizas, J. M. (2020). CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. Springer Nature.https://doi.org/10.1038/s41588-020-00712-y 

Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., &; Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. Springer Nature.https://doi.org/10.1134/S0026893320050088 

Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., &; Alkalaeva, E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. Russian Academy of Sciences.https://doi.org/10.31857/S0026898420050080 

Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O., &; Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLT. In Proceedings of 1st International Electronic Conference on Microbiology. Virtual: MDPI.https://doi.org/10.3390/ecm2020-07116 

Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh, T. V., Guglya, E. B.,https://doi.org/10.1038/s41587-020-0500-9__Sarkisyan, K. S. (2020). Plants with genetically encoded autoluminescence. Nature Biotechnology. Springer Nature.https://doi.org/10.1038/s41587-020-0500-9 

Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S.,https://doi.org/10.1371/journal.pgen.1008079__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 

Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S.,https://doi.org/10.1371/journal.pgen.1008079.s011__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 

Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S.,https://doi.org/10.1371/journal.pgen.1008079.s011__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 

Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S.,https://doi.org/10.1371/journal.pgen.1008079.s010__Kondrashov, F. (2019). Multiple alignment of Hi orthologues. Public Library of Science.https://doi.org/10.1371/journal.pgen.1008079.s010 

Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., &; Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. Springer Nature.https://doi.org/10.1038/s41564-019-0412-y 

Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov, E.,https://doi.org/10.6084/m9.figshare.9808772.v1__Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature.https://doi.org/10.6084/m9.figshare.9808772.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808760.v1__Gelfand, M. S. (2019). Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature.https://doi.org/10.6084/m9.figshare.9808760.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808850.v1__Gelfand, M. S. (2019). Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature.https://doi.org/10.6084/m9.figshare.9808850.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808802.v1__Gelfand, M. S. (2019). Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature.https://doi.org/10.6084/m9.figshare.9808802.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808814.v1__Gelfand, M. S. (2019). Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature.https://doi.org/10.6084/m9.figshare.9808814.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808820.v1__Gelfand, M. S. (2019). Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature.https://doi.org/10.6084/m9.figshare.9808820.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808826.v1__Gelfand, M. S. (2019). Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature.https://doi.org/10.6084/m9.figshare.9808826.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808835.v1__Gelfand, M. S. (2019). Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature.https://doi.org/10.6084/m9.figshare.9808835.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808841.v1__Gelfand, M. S. (2019). Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature.https://doi.org/10.6084/m9.figshare.9808841.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.1186/s12864-019-6059-5__Gelfand, M. S. (2019). Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. BioMed Central.https://doi.org/10.1186/s12864-019-6059-5 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808859.v1__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.https://doi.org/10.6084/m9.figshare.9808859.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808907.v1__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.https://doi.org/10.6084/m9.figshare.9808907.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808865.v1__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.https://doi.org/10.6084/m9.figshare.9808865.v1 

Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E.,https://doi.org/10.6084/m9.figshare.9808886.v1__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.https://doi.org/10.6084/m9.figshare.9808886.v1 

Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A.,https://doi.org/10.1038/s41587-019-0333-6__Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. Springer Nature.https://doi.org/10.1038/s41587-019-0333-6 

Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A.,https://doi.org/10.5281/ZENODO.2025846__Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo.https://doi.org/10.5281/ZENODO.2025846 

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 

Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M.,https://doi.org/10.1073/pnas.1803615115__Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences.https://doi.org/10.1073/pnas.1803615115 

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. BioMed Central.https://doi.org/10.1186/s13059-018-1434-0 

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.https://doi.org/10.6084/m9.figshare.6401414.v1 

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.https://doi.org/10.6084/m9.figshare.6401390.v1 

Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M.,https://doi.org/10.1093/bioinformatics/bty340__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 

Pavan, A., Martins, F., Santos, F., Ditchfield, A., &; Fernandes Redondo, R. A. (2011). Patterns of diversification in two species of short-tailed bats (Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests. Biological Journal of the Linnean Society. Wiley-Blackwell.https://doi.org/10.1111/j.1095-8312.2010.01601.x