Georgii Bazykin

Biography

Head of Sector of Molecular Evolution, Kharkevitch Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia, 2007–present Leading researcher, Lomonosov Moscow State University, Moscow, Russia, 2011–present Senior lecturer, Lomonosov Moscow State University, Moscow, Russia, 2008–present Short-term scholar, University of Michigan, Ann Arbor, 2008 (3 months), 2009 (2 months) Education 2002–2007 Princeton University, Princeton, New Jersey, USA PhD in Ecology and Evolution Advisors: Dr. Simon A. Levin, Dr. Alexey S. Kondrashov Dissertation: Natural selection in sequence evolution: genome-scale, parsimony-based approach 1996–2001 Moscow State University, Moscow, Russia Diploma (B.S.) in Biology (subfield: vertebrate zoology) Honours Thesis: The spatial structure of rodent community in the North-Eastern Cis-Caspian Region Born May 8, 1979 in Moscow, Russia. Phone +7 (903) 975-7211 Fax +7 (495) 650-0579 Email gbazykin@iitp.ru Russian Academy of Sciences Institute for Information Transmission Problems 127994, GSP-4, Moscow, Russia Bol'shoi Karetnyi per., 19 Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University 119992, Moscow, Russia CV: Georgii A. Bazykin Page 2 of 7 Teaching experience 2010–present 6 current graduate students (Vladimir Seplyarskiy, Olga Vakhrusheva, Maria Baranova, Nadezhda Terekhanova, Ksenia Lezhnina, Galya Klink); 2 former graduate students (Sergey Naumenko, PhD 2014; Eugene Leushkin, PhD 2014). 2008–present Advised 8 junior theses (Anna Vakhrusheva, Maria Baranova, Nadezhda Terekhanova, Ksenia Lezhnina, Irina Garanina, Alexandra Bezmenova, Ksenia Safina, Ksenia Khudyakova) and 7 senior theses (Vladimir Seplyarskiy, Eugene Leushkin, Maria Baranova, Nadezhda Terekhanova, Alexandra Akhmadulina, Ksenia Lezhnina, Nadezhda Potapova). 2012–present Developed curriculum and teaching (between 2012-2013, jointly with A. Markov) a graduate course: Evolutionary Biology (Yandex School of Data Analysis, since 2014 – Moscow School of Bioinformatics) 2010–present Developed curriculum and teaching an undergraduate course: Evolutionary Genomics (Faculty of Bioengineering and Bioinformatics, Moscow State University) 2014 Visiting lecturer and co-instructor, undergraduate field course: Molecular Biology (White Sea Biological Station, for the students of the Faculty of Bioengineering and Bioinformatics, Moscow State University) 2011–2013 Developed curriculum and teaching (jointly with A. Kondrashov) an undergraduate course: Evolutionary Biology (Faculty of Bioengineering and Bioinformatics, Moscow State University) 2007–2010 Developed curriculum and teaching (jointly with V. Ramensky) an undergraduate course: Evolutionary and Medical Genomics (Faculty of Bioengineering and Bioinformatics, Moscow State University) 2007–2015 Multiple invited public lectures throughout Russia (geography: Moscow and vicinity, Dubna, Chernogolovka, Puschino, Novosibirsk, Petrozavodsk, Rostov on Don, Saint Petersburg, White Sea Biological Station, Surgut, Tomsk, Yakutsk) 2007–2015 Multiple lectures and classes for undergraduate and high school students throughout Russia 2007–2015 Multiple master classes for school teachers throughout Russia 2007 Guest lecturer: EEB 320/MOL 330: Molecular Evolutionary Genetics, Princeton undergraduate course 2006 Teaching assistant and guest lecturer, EEB 320/MOL 330: Molecular Evolutionary Genetics, Princeton undergraduate course 2003 Teaching assistant, EEB/MOL 211: The Biology of Organisms, Princeton undergraduate course 1998 Guest lecturer in Children's Summer Ecological School, Moscow, Russia Additional research experience 1999–2002 Field researcher on behaviour and social demography (1999-2002) and community ecology (2001-2002) of rodent species in the Kalmykia semidesert, Russia 1995–2001 Field research assistant in multiple research projects CV: Georgii A. Bazykin Page 3 of 7 Peer-reviewed publications ___________________ 34. Bazykin GA. Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins. Biology Letters, in print. 33. Baranova MA, Logacheva MD, Penin AA, Seplyarskiy VB, Safonova YY, Naumenko SA, Klepikova AV, Gerasimov ES, Bazykin GA, James TY, Kondrashov AS. Extraordinary genetic diversity in a wood decay mushroom. Molecular Biology and Evolution pii:msv153 [Epub ahead of print], 2015. 32. Neverov AD, Kryazhimskiy S, Plotkin JB, Bazykin GA. Coordinated Evolution of Influenza A Surface Proteins. PLOS Genetics 11(8):e1005404, 2015. 31. Hayward AD, Virpi L, Bazykin GA. Fitness consequences of advanced ancestral age over three generations in humans. PLOS One 10(6):e0128197, 2015. 30. Kolbasova GD, Zalevsky AO, Gafurov AR, Gusev PO, Ezhova MA, Zheludkevich AA, Konovalova OP, Kotlov NU, Lanina NO, Lapashina AS, Medvedev DO, Nosikova KS, Nuzhdina EO, Bazykin GA, Neretina TV. A new species of Cyanea jellyfish sympatric to C. capillata in the White Sea. Polar Biology 38:1439–1451, 2015. 29. Popadin KY, Gutierrez-Arcelus M, Lappalainen T, Buil A, Steinberg J, Nikolaev SI, Lukowski SW, Bazykin GA, Seplyarskiy VB, Ioannidis P, Zdobnov EM, Dermitzakis ET, Antonarakis SE. Gene Age Predicts the Strength of Purifying Selection Acting on Gene Expression Variation in Humans. American Journal of Human Genetics 95(6):660-74, 2014. 28. Terekhanova NV, Logacheva MD, Penin AA, Neretina TV, Barmintseva AE, Bazykin GA, Kondrashov AS, Mugue NS. Fast Evolution from Precast Bricks: Genomics of Young Freshwater Populations of Threespine Stickleback Gasterosteus aculeatus. PLOS Genetics 10(10):e1004696, 2014. 27. Denisov SV, Bazykin GA, Sutormin R, Favorov AV, Mironov AA, Gelfand MS, Kondrashov AS. Weak negative and positive selection and the drift load at splice sites. Genome Biology and Evolution 6(6):1437-47, 2014. 26. Neverov AD, Lezhnina KV, Kondrashov AS, Bazykin GA. Intrasubtype reassortments cause adaptive amino acid replacements in H3N2 influenza genes. PLOS Genetics 10(1):e1004037, 2014. 25. Flot JF, ..., Bazykin GA, ..., et al. (39 co-authors). Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature 500(7463):453-7, 2013. 24. Kurmangaliyev YZ, Sutormin RA, Naumenko SA, Bazykin GA, Gelfand MS. Functional implications of splicing polymorphisms in the human genome. Human Molecular Genetics 22(17):3449-59, 2013. 23. Leushkin EV, Bazykin GA. Short indels are subject to insertion-biased gene conversion. Evolution 67(9):2604-13, 2013. 22. Terekhanova NV, Bazykin GA, Neverov A, Kondrashov AS, Seplyarskiy VB. Prevalence of multinucleotide replacements in evolution of primates and Drosophila. Molecular Biology and Evolution 30(6):1315-25, 2013. 21. Vakhrusheva OA, Bazykin GA, Kondrashov AS. Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation. Genome Biology and Evolution 5(3):532-41, 2013. 20. Leushkin EV, Bazykin GA, Kondrashov AS. Strong Mutational Bias Toward Deletions in the Drosophila melanogaster Genome Is Compensated by Selection. Genome Biology and Evolution 5(3):514-24, 2013. 19. Bazykin GA, Kondrashov AS. Major role of positive selection in the evolution of conservative segments of Drosophila proteins. Proceedings of the Royal Society B (Biological Sciences) 279(1742):3409-17, 2012. CV: Georgii A. Bazykin Page 4 of 7 18. Naumenko SA, Kondrashov AS, Bazykin GA. Fitness conferred by replaced amino acids declines with time. Biology Letters 8(5):825-8, 2012. 17. Leushkin EV, Bazykin GA, Kondrashov AS. Insertions and deletions trigger adaptive walks in Drosophila proteins. Proceedings of the Royal Society B (Biological Sciences) 279(1740):3075-82, 2012. 16. Seplyarskiy VB, Kharchenko P, Kondrashov AS, Bazykin GA. Heterogeneity of the Transition/Transversion Ratio in Drosophila and Hominidae Genomes. Molecular Biology and Evolution 29(8):1943-55, 2012. 15. Bazykin GA, Kondrashov AS. Detecting past positive selection through ongoing negative selection. Genome Biology and Evolution 3:1006-13, 2011. 14. Vakhrusheva AA, Kazanov MD, Mironov AA, Bazykin GA. Evolution of prokaryotic genes by shift of stop codons. Journal of Molecular Evolution 72(2):138-46, 2011. 13. Kryazhimskiy S, Dushoff J, Bazykin G, Plotkin J. Prevalence of epistasis in the evolution of influenza A surface proteins. PLoS Genetics 7(2):e1001301, 2011. 12. Bazykin G, Kochetov A. Alternative translation start sites are conserved in eukaryotic genomes. Nucleic Acids Research 39(2):567-77, 2011. 11. Vishnoi A, Kryazhimskiy S, Bazykin G, Hannenhalli S, Plotkin J. Young proteins experience more variable selection pressures than old proteins. Genome Research 20(11):1574-81, 2010. 10. Donmez N*, Bazykin G*, Brudno M, Kondrashov A. Polymorphism due to multiple amino acid substitutions at a codon site within Ciona savignyi. Genetics 181:685–690, 2009. * equal contribution 9. Kryazhimskiy S, Bazykin G, Plotkin J, Dushoff J. Directionality in the evolution of influenza A hemagglutinin. Proceedings of the Royal Society B (Biological Sciences) 275(1650):2455– 2464, 2008. 8. Kryazhimskiy S, Bazykin G, Dushoff J. Natural selection for nucleotide usage at synonymous and non-synonymous sites in the influenza A genes. Journal of Virology 82(10): 4938–4945, 2008. 7. Bazykin G, Kondrashov F, Brudno M, Poliakov A, Dubchak I, Kondrashov A. Extensive parallelism in protein evolution. Biology Direct 2:20, 2007. 6. Bazykin G, Dushoff J, Levin S, Kondrashov A. Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites. Proceedings of the National Academy of Sciences of the United States of America 103:19396– 19401, 2006. 5. Kovaleva G, Bazykin G, Brudno M, Gelfand M. Comparative genomics of transcriptional regulation in yeasts and its application to identification of a candidate alpha-isopropylmalate transporter. Journal of Bioinformatics and Computational Biology 4(5):981–998, 2006. 4. Bazykin G, Kondrashov A. Rate of promoter class turn-over in yeast evolution. BMC Evolutionary Biology 10;6(1):14, 2006. 3. Bazykin G, Ogurtsov A, Kondrashov A. Change in CpG context is a leading cause of correlation between rates of non-synonymous and synonymous substitutions in rodents. In: Bioinformatics of Genome Regulation and Structure II, eds. N Kolchanov et al., Springer, 2006. 2. Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. Positive selection at sites of multiple amino acid replacements since rat–mouse divergence. Nature 429:558–562, 2004. 1. Tchabovsky A, Bazykin G. Females delay dispersal and breeding in a solitary gerbil Meriones tamariscinus. Journal of Mammalogy 85(1):105–112, 2004.

Research Interest

evolutionary biology comparative and population genomics viral evolution