Yurtseven, Alper, Sofia Buyanova, Amay Ajaykumar A. Agrawal, Olga Bochkareva, and Olga V V. Kalinina. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.”https://doi.org/10.1186/s12866-023-03147-7__BMC Microbiology. Springer Nature, 2023.https://doi.org/10.1186/s12866-023-03147-7 .

Zabelkin, Alexey, Yulia Yakovleva, Olga Bochkareva, and Nikita Alexeev. “PaReBrick: PArallel REarrangements and BReaks Identification Toolkit.”https://doi.org/10.1093/bioinformatics/btab691__Bioinformatics. Oxford Academic, 2022.https://doi.org/10.1093/bioinformatics/btab691 .

Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics for the COVID-19 Response and Future Pandemics.”https://doi.org/10.1038/s41592-022-01444-z__Nature Methods. Springer Nature, 2022.https://doi.org/10.1038/s41592-022-01444-z .

Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.”https://doi.org/10.1038/s41598-022-10827-3__Scientific Reports. Springer Nature, 2022.https://doi.org/10.1038/s41598-022-10827-3 .

Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.”https://doi.org/10.7554/elife.75842__ELife. eLife Sciences Publications, 2022.https://doi.org/10.7554/elife.75842 .

Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.”https://doi.org/10.1186/s13059-022-02711-0__Genome Biology. BioMed Central, 2022.https://doi.org/10.1186/s13059-022-02711-0 .

Byazrova, Maria G., Ekaterina A. Astakhova, Aygul Minnegalieva, Maria M. Sukhova, Artem A. Mikhailov, Alexey G. Prilipov, Andrey A. Gorchakov, and Alexander V. Filatov. “Anti-Ad26 Humoral Immunity Does Not Compromise SARS-COV-2 Neutralizing Antibody Responses Following Gam-COVID-Vac Booster Vaccination.”https://doi.org/10.1038/s41541-022-00566-x__Npj Vaccines. Springer Nature, 2022.https://doi.org/10.1038/s41541-022-00566-x .

Baumgartner, Maximilian, Rebecca Zirnbauer, Sabine Schlager, Daniel Mertens, Nikolaus Gasche, Barbara Sladek, Craig Herbold, et al. “Atypical Enteropathogenic E. Coli Are Associated with Disease Activity in Ulcerative Colitis.”https://doi.org/10.1080/19490976.2022.2143218__Gut Microbes. Taylor &; Francis, 2022.https://doi.org/10.1080/19490976.2022.2143218 .

Chhugani, Karishma, Alina Frolova, Yuriy Salyha, Andrada Fiscutean, Oksana Zlenko, Sanita Reinsone, Walter W. Wolfsberger, et al. “Remote Opportunities for Scholars in Ukraine.”https://doi.org/10.1126/science.adg0797__Science. American Association for the Advancement of Science, 2022.https://doi.org/10.1126/science.adg0797 .

Pivoluska, Matej, Martin Plesch, Máté Farkas, Natalia Ruzickova, Clara Flegel, Natalia Herrera Valencia, Will Mccutcheon, Mehul Malik, and Edgar A. Aguilar. “Semi-Device-Independent Random Number Generation with Flexible Assumptions.”https://doi.org/10.1038/s41534-021-00387-1__Npj Quantum Information. Springer Nature, 2021.https://doi.org/10.1038/s41534-021-00387-1 .

Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev, Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva. “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.”https://doi.org/10.3389/fmicb.2021.628622__Frontiers in Microbiology. Frontiers, 2021.https://doi.org/10.3389/fmicb.2021.628622 .

Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The Limits of Normal Approximation for Adult Height.”https://doi.org/10.1038/s41431-021-00836-7__European Journal of Human Genetics. Springer Nature, 2021.https://doi.org/10.1038/s41431-021-00836-7 .

Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate of Vaccine-Resistant Strains.”https://doi.org/10.1038/s41598-021-95025-3__Scientific Reports. Springer Nature, 2021.https://doi.org/10.1038/s41598-021-95025-3 .

Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing and DNA Damage Response in Plants.”https://doi.org/10.3389/fpls.2020.00091__Frontiers in Plant Science. Frontiers, 2020.https://doi.org/10.3389/fpls.2020.00091 .

Plesch, Martin, Samuel Plesník, and Natalia Ruzickova. “The IYPT and the ‘Ring Oiler’ Problem.”https://doi.org/10.1088/1361-6404/ab6414__European Journal of Physics. IOP Publishing, 2020.https://doi.org/10.1088/1361-6404/ab6414 .

Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.”https://doi.org/10.1038/s41598-020-65406-1__Scientific Reports. Springer Nature, 2020.https://doi.org/10.1038/s41598-020-65406-1 .

Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological Systems.”https://doi.org/10.1134/S0026893320040111__Molecular Biology. Springer Nature, 2020.https://doi.org/10.1134/S0026893320040111 .

Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological systems.”https://doi.org/10.31857/S0026898420040126__Molekuliarnaia biologiia. Russian Academy of Sciences, 2020.https://doi.org/10.31857/S0026898420040126 .

Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner, Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry Nhttps://doi.org/10.1093/bioinformatics/btz841__Ivankov. “HypercubeME: Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.”https://doi.org/10.1093/bioinformatics/btz841__Bioinformatics. Oxford Academic, 2020.https://doi.org/10.1093/bioinformatics/btz841 .

Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom, and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact Data and Automatic Feature Extraction.”https://doi.org/10.1038/s41588-020-00712-y__Nature Genetics. Springer Nature, 2020.https://doi.org/10.1038/s41588-020-00712-y .

Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation Termination Efficiency in Eukaryotes.”https://doi.org/10.1134/S0026893320050088__Molecular Biology. Springer Nature, 2020.https://doi.org/10.1134/S0026893320050088 .

Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation termination efficiency in eukaryotes.”https://doi.org/10.31857/S0026898420050080__Molekuliarnaia biologiia. Russian Academy of Sciences, 2020.https://doi.org/10.31857/S0026898420050080 .

Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova, Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta Associata GLT.”https://doi.org/10.3390/ecm2020-07116__In Proceedings of 1st International Electronic Conference on Microbiology. MDPI, 2020.https://doi.org/10.3390/ecm2020-07116 .

Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer, Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva, et al. “Plants with Genetically Encoded Autoluminescence.”https://doi.org/10.1038/s41587-020-0500-9__Nature Biotechnology. Springer Nature, 2020.https://doi.org/10.1038/s41587-020-0500-9 .

Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.”https://doi.org/10.1371/journal.pgen.1008079__PLoS Genetics. Public Library of Science, 2019.https://doi.org/10.1371/journal.pgen.1008079 .

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.”https://doi.org/10.1371/journal.pgen.1008079.s011__Public Library of Science, 2019.https://doi.org/10.1371/journal.pgen.1008079.s011 .

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.”https://doi.org/10.1371/journal.pgen.1008079.s011__Public Library of Science, 2019.https://doi.org/10.1371/journal.pgen.1008079.s011 .

Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple Alignment of Hi Orthologues.”https://doi.org/10.1371/journal.pgen.1008079.s010__Public Library of Science, 2019.https://doi.org/10.1371/journal.pgen.1008079.s010 .

Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.”https://doi.org/10.1038/s41564-019-0412-y__Nature Microbiology. Springer Nature, 2019.https://doi.org/10.1038/s41564-019-0412-y .

Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.”https://doi.org/10.6084/m9.figshare.9808772.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808772.v1 .

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 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.”https://doi.org/10.6084/m9.figshare.9808760.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808760.v1 .

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 20 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.”https://doi.org/10.6084/m9.figshare.9808850.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808850.v1 .

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 15 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.”https://doi.org/10.6084/m9.figshare.9808802.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808802.v1 .

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 16 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.”https://doi.org/10.6084/m9.figshare.9808814.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808814.v1 .

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 17 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.”https://doi.org/10.6084/m9.figshare.9808820.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808820.v1 .

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 18 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.”https://doi.org/10.6084/m9.figshare.9808826.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808826.v1 .

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 19 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.”https://doi.org/10.6084/m9.figshare.9808835.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808835.v1 .

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 1 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.”https://doi.org/10.6084/m9.figshare.9808841.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808841.v1 .

Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.”https://doi.org/10.1186/s12864-019-6059-5__BMC Genomics. BioMed Central, 2019.https://doi.org/10.1186/s12864-019-6059-5 .

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.”https://doi.org/10.6084/m9.figshare.9808859.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808859.v1 .

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.”https://doi.org/10.6084/m9.figshare.9808907.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808907.v1 .

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.”https://doi.org/10.6084/m9.figshare.9808865.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808865.v1 .

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.”https://doi.org/10.6084/m9.figshare.9808886.v1__Springer Nature, 2019.https://doi.org/10.6084/m9.figshare.9808886.v1 .

Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.”https://doi.org/10.1038/s41587-019-0333-6__Nature Biotechnology. Springer Nature, 2019.https://doi.org/10.1038/s41587-019-0333-6 .

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.”https://doi.org/10.5281/ZENODO.2025846__Zenodo, 2018.https://doi.org/10.5281/ZENODO.2025846 .

Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.”https://doi.org/10.1093/gbe/evy049__Genome Biology and Evolution. Oxford University Press, 2018.https://doi.org/10.1093/gbe/evy049 .

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.”https://doi.org/10.1073/pnas.1803615115__Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018.https://doi.org/10.1073/pnas.1803615115 .

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.”https://doi.org/10.1186/s13059-018-1434-0__Genome Biology. BioMed Central, 2018.https://doi.org/10.1186/s13059-018-1434-0 .

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.”https://doi.org/10.6084/m9.figshare.6401414.v1__Springer Nature, 2018.https://doi.org/10.6084/m9.figshare.6401414.v1 .

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.”https://doi.org/10.6084/m9.figshare.6401390.v1__Springer Nature, 2018.https://doi.org/10.6084/m9.figshare.6401390.v1 .

Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.”https://doi.org/10.1093/bioinformatics/bty340__Bioinformatics. Oxford University Press , 2018.https://doi.org/10.1093/bioinformatics/bty340 .

Pavan, Ana, Felipe Martins, Fabrício Santos, Albert Ditchfield, and Rodrigo A Fernandes Redondo. “Patterns of Diversification in Two Species of Short-Tailed Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian Rainforests.”https://doi.org/10.1111/j.1095-8312.2010.01601.x__Biological Journal of the Linnean Society. Wiley-Blackwell, 2011.https://doi.org/10.1111/j.1095-8312.2010.01601.x .