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56 Publications


2024 | Journal Article | IST-REx-ID: 15179 | OA
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.
[Published Version] View | Files available | DOI
 

2023 | Journal Article | IST-REx-ID: 12758 | OA
Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I. S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact of single mutations on protein stability and function. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0282689
[Published Version] View | Files available | DOI | WoS
 

2023 | Journal Article | IST-REx-ID: 13164 | OA
Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39317-4
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2023 | Journal Article | IST-REx-ID: 13976 | OA
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.
[Published Version] View | DOI | Download Published Version (ext.) | WoS | PubMed | Europe PMC
 

2023 | Journal Article | IST-REx-ID: 14716 | OA
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
[Published Version] View | Files available | DOI | PubMed | Europe PMC
 

2022 | Journal Article | IST-REx-ID: 10927 | OA
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
[Published Version] View | Files available | DOI | WoS
 

2022 | Journal Article | IST-REx-ID: 11187 | OA
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 | OA
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
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2022 | Journal Article | IST-REx-ID: 11448 | OA
Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.75842
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2022 | Journal Article | IST-REx-ID: 11587 | OA
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.
[Published Version] View | Files available | DOI | WoS
 

2022 | Journal Article | IST-REx-ID: 12131 | OA
Byazrova, M. G., Astakhova, E. A., Minnegalieva, A., Sukhova, M. M., Mikhailov, A. A., Prilipov, A. G., … 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
[Published Version] View | Files available | DOI | WoS | PubMed | Europe PMC
 

2022 | Journal Article | IST-REx-ID: 12173 | OA
Baumgartner, M., Zirnbauer, R., Schlager, S., Mertens, D., Gasche, N., Sladek, B., … 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
[Published Version] View | Files available | DOI | WoS
 

2022 | Journal Article | IST-REx-ID: 12116 | OA
Chhugani, K., Frolova, A., Salyha, Y., Fiscutean, A., Zlenko, O., Reinsone, S., … Mangul, S. (2022). Remote opportunities for scholars in Ukraine. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adg0797
[Published Version] View | DOI | Download Published Version (ext.) | WoS
 

2021 | Journal Article | IST-REx-ID: 9255 | OA
Pivoluska, M., Plesch, M., Farkas, M., Ruzickova, N., Flegel, C., Valencia, N. H., … 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
[Published Version] View | Files available | DOI | WoS
 

2021 | Journal Article | IST-REx-ID: 9380 | OA
Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O., Alexeev, N., … 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
[Published Version] View | Files available | DOI | WoS
 

2021 | Journal Article | IST-REx-ID: 9910 | OA
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
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2021 | Journal Article | IST-REx-ID: 9905 | OA
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
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2020 | Journal Article | IST-REx-ID: 7603 | OA
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
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2020 | Journal Article | IST-REx-ID: 7622 | OA
Plesch, M., Plesník, S., & Ruzickova, N. (2020). The IYPT and the “Ring Oiler” problem. European Journal of Physics. IOP Publishing. https://doi.org/10.1088/1361-6404/ab6414
[Published Version] View | Files available | DOI | WoS | arXiv
 

2020 | Journal Article | IST-REx-ID: 7931 | OA
Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-020-65406-1
[Published Version] View | Files available | DOI | WoS
 

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