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56 Publications
2024 | Journal Article | IST-REx-ID: 15179 | 
Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances. 10(10), adk1992.
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2023 | Journal Article | IST-REx-ID: 12758 |
Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. 2023;18(3). doi:10.1371/journal.pone.0282689
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2023 | Journal Article | IST-REx-ID: 13164 |
Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 2023;14. doi:10.1038/s41467-023-39317-4
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2023 | Journal Article | IST-REx-ID: 13976 |
Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience. 12.
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2023 | Journal Article | IST-REx-ID: 14716 |
Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 2023;23(1). doi:10.1186/s12866-023-03147-7
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2022 | Journal Article | IST-REx-ID: 10927 |
Zabelkin A, Yakovleva Y, Bochkareva O, Alexeev N. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics. 2022;38(2):357-363. doi:10.1093/bioinformatics/btab691
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2022 | Journal Article | IST-REx-ID: 11187 |
Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 19(4), 374–380.
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2022 | Journal Article | IST-REx-ID: 11344 |
Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific Reports. 2022;12. doi:10.1038/s41598-022-10827-3
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2022 | Journal Article | IST-REx-ID: 11448 |
Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 2022;11. doi:10.7554/elife.75842
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2022 | Journal Article | IST-REx-ID: 11587 |
Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. 2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 23, 149.
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2022 | Journal Article | IST-REx-ID: 12131 |
Byazrova MG, Astakhova EA, Minnegalieva A, et al. Anti-Ad26 humoral immunity does not compromise SARS-COV-2 neutralizing antibody responses following Gam-COVID-Vac booster vaccination. npj Vaccines. 2022;7. doi:10.1038/s41541-022-00566-x
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2022 | Journal Article | IST-REx-ID: 12173 |
Baumgartner M, Zirnbauer R, Schlager S, et al. Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis. Gut Microbes. 2022;14(1). doi:10.1080/19490976.2022.2143218
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2022 | Journal Article | IST-REx-ID: 12116 |
Chhugani K, Frolova A, Salyha Y, et al. Remote opportunities for scholars in Ukraine. Science. 2022;378(6626):1285-1286. doi:10.1126/science.adg0797
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2021 | Journal Article | IST-REx-ID: 9255 |
Pivoluska M, Plesch M, Farkas M, et al. Semi-device-independent random number generation with flexible assumptions. npj Quantum Information. 2021;7. doi:10.1038/s41534-021-00387-1
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2021 | Journal Article | IST-REx-ID: 9380 |
Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.628622
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2021 | Journal Article | IST-REx-ID: 9910 |
Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation for adult height. European Journal of Human Genetics. 2021;29(7):1082-1091. doi:10.1038/s41431-021-00836-7
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2021 | Journal Article | IST-REx-ID: 9905 |
Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains. Scientific Reports. 2021;11(1). doi:10.1038/s41598-021-95025-3
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2020 | Journal Article | IST-REx-ID: 7603 |
Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.00091
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2020 | Journal Article | IST-REx-ID: 7622 |
Plesch M, Plesník S, Ruzickova N. The IYPT and the “Ring Oiler” problem. European Journal of Physics. 2020;41(3). doi:10.1088/1361-6404/ab6414
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2020 | Journal Article | IST-REx-ID: 7931 |
Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 2020;10. doi:10.1038/s41598-020-65406-1
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2020 | Journal Article | IST-REx-ID: 8320
Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molecular Biology. 2020;54(4):475-484. doi:10.1134/S0026893320040111
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2020 | Journal Article | IST-REx-ID: 8321
Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126
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2020 | Journal Article | IST-REx-ID: 8645 |
Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million combinatorially complete datasets from a single experiment. Bioinformatics. 2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841
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2020 | Journal Article | IST-REx-ID: 8707
Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y
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2020 | Journal Article | IST-REx-ID: 8700
Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molecular Biology. 2020;54(5):739-748. doi:10.1134/S0026893320050088
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2020 | Journal Article | IST-REx-ID: 8701
Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes. Molekuliarnaia biologiia. 2020;54(5):837-848. doi:10.31857/S0026898420050080
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2020 | Conference Paper | IST-REx-ID: 15071 |
Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata GLS2T. In: Proceedings of 1st International Electronic Conference on Microbiology. MDPI; 2020. doi:10.3390/ecm2020-07116
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2020 | Journal Article | IST-REx-ID: 7889 |
Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV, Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV, Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D, Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV, Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded autoluminescence. Nature Biotechnology. 38, 944–946.
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2019 | Journal Article | IST-REx-ID: 6419 |
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
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2019 | Research Data Reference | IST-REx-ID: 9790
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
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2019 | Research Data Reference | IST-REx-ID: 9797
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
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2019 | Research Data Reference | IST-REx-ID: 9789
Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3 orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010
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2019 | Journal Article | IST-REx-ID: 6506 |
Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y
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2019 | Research Data Reference | IST-REx-ID: 9731 |
Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808772.v1
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2019 | Research Data Reference | IST-REx-ID: 9783 |
Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808760.v1
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2019 | Research Data Reference | IST-REx-ID: 9897 |
Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808850.v1
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2019 | Research Data Reference | IST-REx-ID: 9890 |
Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808802.v1
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2019 | Research Data Reference | IST-REx-ID: 9892 |
Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808814.v1
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2019 | Research Data Reference | IST-REx-ID: 9893 |
Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808820.v1
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2019 | Research Data Reference | IST-REx-ID: 9894 |
Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808826.v1
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2019 | Research Data Reference | IST-REx-ID: 9895 |
Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808835.v1
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2019 | Research Data Reference | IST-REx-ID: 9896 |
Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808841.v1
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2019 | Journal Article | IST-REx-ID: 6898 |
Sigalova OM, Chaplin AV, Bochkareva O, et al. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 2019;20(1). doi:10.1186/s12864-019-6059-5
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2019 | Research Data Reference | IST-REx-ID: 9898 |
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:10.6084/m9.figshare.9808859.v1
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2019 | Research Data Reference | IST-REx-ID: 9901 |
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:10.6084/m9.figshare.9808907.v1
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2019 | Research Data Reference | IST-REx-ID: 9899 |
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:10.6084/m9.figshare.9808865.v1
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2019 | Research Data Reference | IST-REx-ID: 9900 |
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:10.6084/m9.figshare.9808886.v1
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2019 | Journal Article | IST-REx-ID: 7181 |
Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470. doi:10.1038/s41587-019-0333-6
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2018 | Research Data Reference | IST-REx-ID: 13059 |
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:10.5281/ZENODO.2025846
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2018 | Journal Article | IST-REx-ID: 384 |
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
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