Publications

[ ^# – equal contribution. ]

Peer-reviewed publications

• Alper Yurtseven, Sofia Buyanova, Amay A. Agrawal, Olga O. Bochkareva & Olga V. Kalinina. Machine learning and phylogenetic analysis improves predicting antibiotic resistance in M. tuberculosis BMC Microbiol 23, 404 (2023) (DOI)
• Maximilian Baumgartner, Rebecca Zirnbauer, Sabine Schlager, Daniel Mertens, Nikolaus Gasche, Barbara Sladek, Craig Herbold, Olga Bochkareva, Vera Emelianenko, Harald Vogelsang, Michaela Lang, Anton Klotz, Birgit Moik, Athanasios Makristathis, David Berry, Stefanie Dabsch, Vineeta Khare, Christoph Gasche. Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis Gut Microbes 2022, Nov 22; 14(1):2143218 (DOI)
• Natalia O Dranenko, Maria Tutukina, Mikhail S. Gelfand, Fyodor Kondrashov, Olga O Bochkareva. Chromosome-encoded IpaH ubiquitin ligases indicate non-human pathogenic Escherichia SciRep 2022 Apr 27, 12:6868 (DOI)
• Alexey Zabelkin, Yulia Yakovleva, Olga Bochkareva^#, Nikita Alexeev^#. PaReBrick: PArallel REarrangements and BReaks identification toolkit. Bioinformatics 2021 Oct 03; 38(2):357-363 DOI
• Zaira Seferbekova, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev, Natalia O. Dranenko, Nikita Alexeev, Mikhail S Gelfand, Olga Bochkareva. High rates of genome rearrangements and pathogenicity of Shigella spp. Frontiers Microbiology 2021 Apr 12; 12:831. (DOI)
• Olga Sigalova, Andrei V Chaplin, Olga O Bochkareva, Pavel V Shelyakin, Vsevolod A Filaretov, Evgeny E Akkuratov, Valentina Burskaya, Mikhail S Gelfand. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics. 2019 Sep 12;20(1):710. (DOI)
• Pavel V Shelyakin^#, Olga O Bochkareva^#, Anna A Karan, Mikhail S Gelfand. Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow. BMC Evol. Biol. 2019. Mar 27;19(1):83. (DOI).
• Olga O Bochkareva, Elena V Moroz, Iakov I Davydov, Mikhail S Gelfand. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 2018 Dec 27;19(1):965. (DOI)
• Olga O Bochkareva, Natalia O Dranenko, Elena S Ocheredko, German M Kanevsky, Yaroslav N Lozinsky, Vera A Khalaycheva, Irena I Artamonova, Mikhail S Gelfand. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 2018 Mar 27;6:e4545. (DOI)

Preprints / under review

• Natalia O Dranenko, Aleksandra D Rodina, Yaroslav V Demenchuk, Mikhail S. Gelfand, Olga O Bochkareva. Evolutionary trajectories of secondary replicons in multipartite genomes bioRxiv 2023 Apr 09: 536151; (DOI)
• Ekaterina V. Vostokova, Natalia O. Dranenko, Mikhail S. Gelfand, Olga O. Bochkareva Genome rearrangements drive evolution of ANK genes in Wolbachia bioRxiv 2023 October 27:563763 (DOI)

Conference proceedings

• Kristina Y. Perevoshchikova , Vera Emelianenko , Mikhail S. Gelfand , Fyodor Kondrashov, Olga O. Bochkareva Evolutionary benefits of bacterial genomes with chromids Moscow Conference on Computational Molecular Biology (MCCMB 2021) (pdf)
• Ariadna A Semenova, Olga O Bochkareva Insertion sequences in B. mallei: adaptation to intracellular lifestyle Moscow Conference on Computational Molecular Biology (MCCMB 2021) (pdf)
• Natalia Dranenko, Maria Tutukina, Olga Bochkareva The Classification of ipaH Genes in Shigella and Enteroinvasive Escherichia Moscow Conference on Computational Molecular Biology (MCCMB 2021) (pdf)
• Vera Emelianenko, Anna Kaznadzey, Maria Tutukina, Olga Bochkareva Two sequence variants of the yjjM gene in the Escherichia coli genomes Moscow Conference on Computational Molecular Biology (MCCMB 2021) (pdf)
• Alexey Zabelkin, Yulia Yakovleva, Olga Bochkareva, Nikita Alexeev Method for detection of parallel adaptation with genome rearrangements in bacterial populations Moscow Conference on Computational Molecular Biology (MCCMB 2021) (pdf)
• Viktoriia Oshurkova, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova, Olga Bochkareva, Viktoria Shcherbakova. “Characterization of Methanosarcina mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation with Bacterium Sphaerochaeta associata GLS2T” Proceedings 2020; 66(1):4. DOI