Home »

Stephen J. O’Brien

Principal investigator

Stephen J. O’Brien served as Chief of the Laboratory of Genomic Diversity at the National Cancer Institute (NCI), National Institutes of Health (NIH) from 1986-2011. In December 2011, he joined the Theodosius Dobzhansky Center for Genome Bioinformatics , St. Petersburg State University as Chief Scientific Officer. His research interests and expertise span human and comparative genomics, genetic epidemiology, HIV/AIDS, retro-virology, bioinformatics biodiversity and species conservation. Dr. O’Brien served as Editor of six editions of Genetic Maps: Locus Maps of Complex Genomes (1980-1993) (Cold Spring Harbor Laboratory Publications); Editor of Journal of Heredity (American Genetics Association) from 1987-2007; Editor of “Atlas of Mammalian Chromosomes” (John Wiley Inc. NYC, 2006) and author of “Tears of the Cheetah And Other Tales From The Genetic Frontier” (St. Martin’s Press NYC, 2004).

Dr. O’Brien received his B.S. in Biology in 1966 from St. Francis College, which presented him with a Distinguished Alumni Award in 1994. In 1971 he earned a Ph.D. in Genetics from Cornell University which honored him as “Andrew Dixon White Endowed Professor at Large” in 1998. Dr. O’Brien has a strong dedication to education, evidenced by his appointments as adjunct professor at twelve universities. He has mentored more than fifteen Ph.D. students and multiple postdoctoral fellows. Since 1996 he has directed an internationally heralded short course sponsored by Smithsonian and American Genetics Association, entitled “Recent Advances in Conservation Genetics”, the most recent (2012) edition at The Smithsonian Tropical Research Institute , Panama.

Vladimir Brukhin

Leading Researcher

In February 2013 Vladimir Brukhin Joined the Theodosius Dobzhansky Center for Genome Bioinformatics after returning from the UK, where he worked as a Senior Research fellow at the School of Biology, University of Edinburgh. His main research interests are in the field of functional genetics, comparative genomics, epigenetics, sexual and asexual plant reproduction, developmental biology and evolution. Currently Dr. Brukhin coordinates the project Genome Russia (http://genomerussia.bio.spbu.ru/?lang=en) main goal of which is creation of the web-based database containing depersonalised information on the whole-genome sequences of at least 2,500 men and women originating from the different regions of Russia, whose ancestors were indigenous to the region for several generations, as well as description of the genome variations in these groups, detection of the features that affect the spread of diseases and creation of a database of medically-relevant genomic variants characteristic to the Russian population. Other projects supervised by Dr. Brukhin are carried out in the frames of 3 year Swiss-Russian collaboration program “Sequencing, Assembly, and Annotation of the Highly Heterozygous Genome of the Apomictic Plant Boechera divaricarpa” and 2-year Russian-Indian program “Fixing hybrid vigor by asexual reproduction-A chemical genetics screen towards harnessing apomixis in flowering plants”. Main goal of the both projects is a better understanding of the molecular basis of apomixis the asexual reproduction of plants through seed, that could become a key ‘enabling technology’ of immense benefit to agriculture, because it would enable the permanent fixation of heterosis in crop plants. Also Dr. Brukhin develops the project “Whole genome methylation analysis in species-specific phenotypes and at the various developmental stages”.

Dr. Brukhin received his Master in Agricultural Chemistry in 1988 from the faculty of Biology and Soil Science, St. Petersburg State University. In 1993 he earned a Ph.D. in Developmental Biology from Komarov Botanical Institute, Russian Academy of Sciences. In 1994 – Dr. Brukhin worked as a trainee at the University of Lublin in Poland where he studied plant developmental biology and microscopy. In 1997-1999 He was a postdoctoral researcher in France and Sweden studying somatic embryogenesis, apoptosis and genes specifically expressed during and after fertilization. In 2000-2006 he worked as a Senior Research Associate at the Department of Plant Developmental Genetics, University of Zurich, Switzerland, where he was responsible for co-ordinating the lab contributions to the multinational EU project EXOTIC (Exon Trapping Insert Consortium) and also he developed an independent research project ‘The Ubiquitin 26S Proteasome Proteolytic Pathway and Plant Reproduction’. At the University of Zurich Dr. Brukhin was a practical instructor for Mittlebaukurs, Plant Developmental Biology. In 2006-2007 he was invited to the University of Illinois at Urbana-Champaign to participate in the project on developmental aspects of posttranslational protein modifications. In 2008-2013 Dr. Brukhin worked in the UK (University of Aberystwyth and University of Edinburgh) where he studied epigenetics, problems of plant cell identity and specialization. In the UK he was also involved in tuition and supervision of undergraduate and PhD students.

List of publications:

  1. Yurchenko A, Yudin N, Aitnazarov R, Plyusnina A, Brukhin V, Soloshenko V, Lhasaranov B, Popov R, Paronyan IA, Plemyashov KV, Larkin DM. (2017) Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds. Heredity. doi: 10.1038/s41437-017-0024-3.

  2. Osadtchiy J. V., Naumova T. N., Brukhin V. B. (2017) APOMIXIS IN THE GENUS BOECHERA (BRASSICACEAE). Bot. J. 102 (12): 1587-1607.

  3. Brukhin V. (2017) Molecular and Genetic Regulation of Apomixis. Russian Journal of Genetics 53(9):1001-1024. doi: 10.1134/S1022795417090046

  4. Brukhin V. (2017) Is sex irreplaceable? Towards the molecular regulation of apomixis. The International Journal of Plant Reproductive Biology. 9(2) Jul., 2017, pp.153-169. doi: 10.14787/ijprb.2017 9.2.153-169

  5. Oleksyk TK, Brukhin V, O’Brien SJ. (2015) Putting Russia on the genome map. Science. 13; 350 (6262): 747.

  6. Oleksyk TK, Brukhin V, O’Brien SJ. (2015) The Genome Russia project: closing the largest remaining omission on the world Genome map. Gigascience; 4:53.

  7. Dobrynin P, Liu S, Tamazian G, Xiong Z, Yurchenko AA, Krasheninnikova K, Kliver S, Schmidt-Küntzel A, Koepfli KP, Johnson W, Kuderna LF, García-Pérez R, Manuel Md, Godinez R, Komissarov A, Makunin A, Brukhin V, Qiu W, Zhou L, Li F, Yi J, Driscoll C, Antunes A, Oleksyk TK, Eizirik E, Perelman P, Roelke M, Wildt D, Diekhans M, Marques-Bonet T, Marker L, Bhak J, Wang J, Zhang G, O’Brien SJ. (2015) Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biol.; 16:277.

  8. Tamazian G, Simonov S, Dobrynin P, Makunin A, Logachev A, Komissarov A, Shevchenko A, Brukhin V, Cherkasov N, Svitin A, Koepfli KP, Pontius J, Driscoll CA, Blackistone K, Barr C, Goldman D, Antunes A, Quilez J, Lorente-Galdos B, Alkan C, Marques-Bonet T, Menotti-Raymond M, David VA, Narfström K, O’Brien SJ.
    (2014) Annotated Features of Domestic Cat-Felis Catus. Gigascience. 3:13

  9. Brukhin V. and Morozova N. (2011) Plant growth and development – basic knowledge and current views. Mathematical Modelling Natural Phenomena, 6 (2): 1- 53.

  10. Brukhin V., Jaciubek, M., Bolaños Carpio A., Kuzmina V., Grossniklaus U. (2011) Female Gametophytic mutants of Arabidopsis thaliana identified in a gene Trap Insertional Mutagenesis Screen, Int. J. Dev. Biol. 55: 73-84.

  11. Dumbliauskas E., Lechner E., Alioua M., Cognat V., Brukhin V., Berger F., Koncz C., Grossniklaus U., Molinier J., Genschik P. (2011) The Arabidopsis CUL4-DDB1 complex interacts with MSI1 and is required to maintain MEA parental imprinting. EMBO J. 30 (4):731-43.

  12. Chekanova J.A., Gregory B.D., Reverdatto S.V., Chen H., Kumar R., Hooker T., Junshi Yazaki J., Li P., Skiba N., Peng Q., Alonso J., Brukhin V., Grossniklaus U., Ecker J.R.; Belostotsky D.A. (2007) Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome. Cell, 131 (7):1340-1353.

  13. Brukhin V., Curtis M.D., Grossniklaus U. (2005) The angiosperm female gametophyte: no longer forgotten generation. Review Current Science, 89 (11).

  14. Brukhin V., Gheyeselinck J., Gagliardini V., Genschik P., Grossniklaus U. (2005) The RPN1 subunit of the 26S proteasome in Arabidopsis is essential for embryogenesis. The Plant Cell, 17 (10): 2723-37.

  15. Thomann A. *, Brukhin V., Dieterle M., Gheyeselinck J., Grossniklaus U. and Genschik P. (2005) Arabidopsis CUL3A and CUL3B genes are essential for normal embryogenesis. The Plant Journal, 43 (3): 437-448.

  16. Brukhin V., Hernould M., Gonzalez N., Chevalier C., Mouras A. (2003) Flower development schedule in tomato Lycopersicon esculentum cv. sweet cherry. Sex. Plant Reproduction. 15 (6): 311-320.

  17. Brukhin V., Clapham D., Elfstrand M., von Arnold S. (2000) Basta tolerance as a selectable and screening marker for transgenic plants of Norway spruce.- Plant Cell Reports, 19: 899-903.

  18. Filonova L.H., Bozhkov P.V., Brukhin V.B., Daniel G., Zhivotovsky B. and von Arnold S. (2000) Two waves of programmed cell death occur during formation and development of somatic embryos in the gymnosperm Norway spruce. J Cell Sci, 113 (24): 4399-4411.

  19. Brukhin V.B., Moleva I.R., Filonova L.H., Grakhov V.P., Blume Ya.B, Bozhkov P.V. (1996) Proliferative activity of callus culture of Taxus baccata in relation to anticancer diterpenoid taxol biosynthesis. Biotechnology Letters (Chapman & Hall, London), vol. 18, N 11, pp. 1309-1314.

  20. Brukhin V.B., Bozhkov P.V. (1996) Female gametophyte development and embryogenesis in Taxus baccata L. – Acta Soc. Bot.Pol., vol. 65, N 1-2, pp. 135-139.

  21. Tchorzewska D., Brukhin V.B., Bednara J. (1996) Organelle layers at meiocyte of Psilotum nudum. – Acta Soc.Bot.Pol., vol. 65, N 1-2, pp. 91-96.

  22. Brukhin.V., Zemanek A. (1996) The manuscripts of Russian translations of the Polish herbal /Zielnik/ (1613) by Syreniusz in St. Petersburg.- Kwartalnik historii nauki i techniki (Warsaw), vol. 41, N 3-4, pp. 189-195.

  23. Brukhin V.B., Batygina T.B. (1994) Embryo culture and somatic embryogenesis in culture of Paeonia anomala L. – Phytomorphology. – v. 44, N 3 & 4. – pp. 151-157.

  24. Brukhin V.B. (2006) Histochemical and immunohistochemical aspects of embryogenesis. In: Embryology of flowering plants Terminology and Concepts. Ed. Prof. T.Batygina. Enfield, NH, USA, Science Publisher Inc. vol. 2 Seed, pp. 568-572.

  25. Batygina T.B., Brukhin V.B. (2006) Embryogenesis in Paeoniaceae. In: Embryology of flowering plants. Terminology and Concepts Ed. Prof. T.Batygina. Enfield, NH, USA, Science Publisher Inc. vol. 2 Seed, pp. 539-543.

Sergey V. Malov

Leading Researcher

Sergey V. Malov graduated from St.-Petersburg State University in 1992. He specialized in Probability Theory and Mathematical Statistics and finished his Ph.D. thesis at St.-Petersburg State University in 1995. Dr. Sergey V. Malov completed postdoctoral program in Survival Analysis at Victor Segalen Bordeaux 2 University in 1997-1998. In 2007 Dr. Sergey V. Malov attended fellowship program in applied statistics and AIDS research at CIRA of Yale University. Dr. Sergey V. Malov is an author of more then 25 scientific works in probability theory and mathematical statistics. During 2001 to present time period he was an invited scientist at Mc Master University (Canada), at Le Havre University (France) and at Otto von Guericke University of Magdeburg. He is reviewer in “AMS mathematical reviews” from 2006. Dr. Sergey V. Malovis giving courses on probability theory, mathematical statistics and random processes theory for bachelor students at St.-Petersburg Electrotechnical University and courses on applied statistics for master students at St.-Petersburg State University.


General interest of Dr. Sergey V.Malov in the project is an application of mathematical methods in genetics. Main interest is to use modern statistical methods in gene discovery. Current interests are following:

(i). Gene wide association study (GWAS). The aim of GWAS is to specify disease association genes. Hundred of thousands SNP variants across a genome are tested on association with the disease by different tests. Different tests based on fixed time point data, longitudinal and survival data are involved in testing process. The aim is to analyze and interpret correctly results of statistical tests simultaneously. The GWAS methods will be applied to discover AIDS restriction genes.

(ii). Whole genome assembling process currently does not lead to exact genomic sequence. The whole genome association with vertebrate species is dependent on accuracy of genome assembling. Some technical aspects of genome assembling, using probabilistic and Monte Carlo methods for genome assembling are among current interests of Dr. Sergey V.Malov in the project.

Current scientific interests:

  • Survival Analysis, Censored Data, Multivariate Rank Statistics
  • Dependence concept. Copulas.
  • Biostatistics, Applications of Multivariate Rank Statistics of Survival Analysis
  • Biostatistics, GLM, Multivariate contingency tables
  • Applications of mathematical and statistical methods in genomic analysis

Current research interests:

  • Data analysis in AIDS research
  • Population genetics, statistical data analysis
  • Application of statistical methods in gene discovery

Teaching experience:

  • Courses on Probability Theory, Math. Statistics, Random Processes, Mathematical Analysis, Linear algebra at St.-Petersburg Electrotechnical University “LETI”;
  • Courses on Probability Theory and Mathematical Statistics at St.-Petersburg State University
  • Special courses “Regression analysis”, “Random Processes in Biology and Medicine”, “Survival Analysis” for specialization “Biostatistics” at St.-Petersburg State University.
  • Special course on Biometrics for student at the char “Biogeography and nature protection” of the Institute of sciences around Earth (SPBU)

Sergei V. Malov: List of publications

  1. Malov, S.V., O’Brien S.J. (2017) Life Table Estimator Revisited. Communications in Statistics – Theory and Methods, Published online (to appear in 2018), DOI: 10.1080/03610926.2017.1335418.
  2. Malov, S.V., Antonik A., Tang M., Berred A., Zeng Yi & O’Brien S.J. (2017) Signal localization: a new approach in signal discovery. Biometrical Journal 59(1), 126 –144. DOI: 10.1002/bimj.201500222.
  3. Malova, I.Yu., Malov, S.V. (2017) On survival categorical methods from grouped right censored data with unobserved status after censoring. In Applied Methods of Statistical Analysis. Nonparametric Methods in Cybernetics and System Analysis. Proceedings of the International Workshop AMSA’17 (Krasnoyarsk, September 18-22, 2017), 136–142.
  4. Bajenova, O., Tolkunova, E., Koshkin, S., Malov, S., Thomas, P., Tomilin, A. and O’Brien, S.J. (2017) The role of the carcinoembryonic antigen receptor in colorectal cancer progression. Journal of Integrative Oncology 6(2), 192. DOI:10.4172/2329-6771.1000192.
  5. Xie, W., Agniel, D., Shevchenko A., Malov, S.V., Svitin, A., Cherkasov, N., Baum, M.K. Campa, A., Gaseitsiwe, S., Bussmann, H., Makhema, J., Marlink,R., Novitsky, V., Lee, T.-H., Cai, T., O’Brien, S.J. and Essex,M. (2017) Genome-Wide Analyses Reveal Gene Influence on HIV Disease Progression and HIV-1C Acquisition in Southern Africa. AIDS Research and Human Retroviruses 33(6), 597– 609.
  6. Kozlov A.P., Skochilov R.V., Toussova O.V., Verevochkin S.V., Krasnoselskikh T.V., Malov S.V., Shaboltas A.V. (2016) HIV incidence and behavioral correlates of HIV acquisition in a cohort of injection drug users in St Petersburg, Russia. Medicine 95(44), e5238, DOI:10.1097/MD.0000000000005238
  7. Malov, S.V. (2015) Copula process, Archimedean. Wiley StatsRef: Statistics Reference Online. pp. 1–7.
  8. Malov, S.V. & O’Brien, S.J. (2015) On survival categorical methods based on an extended actuarial estimator. In Applied Methods of Statistical Analysis. Nonparametric Approach. Proceedings of the International Workshop AMSA’15 (Novosibirsk-Belokuriha, September 14-19, 2015), 169–175.
  9. Svitin, A, Malov, S., Cherkasov, N., Geerts P., Rotkevich, M, Dobrynin P.,
    Shevchenko, A., Guan, Li, Troyer, J., Hendrickson-Lambert, S., Dilks, H.H., Oleksyk, T.K., Donfield, S., Gomperts, E., Jabs, D.A., Sezgin, Efe, Van Natta, M., Harrigan, P.R., Brumme, Z.L. & O’Brien, S.J. (2014), GWATCH: a web platform for automated gene association discovery analysis. GigaScience, 3:18

  10. Malov S.V. & O’Brien S.J (2013) On Survival Categorical Methods with Applications in Epidemiology and AIDS Research. In Applied Methods of Statistical Analysis. Applications in Survival Analysis, Reliability and Quality Control. Proceedings of the International Workshop AMSA’13 (Novosibirsk, September 25-27, 2013), 173–180.
  11. Antonik, A., O’Brien S.J. & Malov, S.V. (2013) Whole Genome Sequence Coverage Estimation Re-examined. In Applied Methods of Statistical Analysis. Applications in Survival Analysis, Reliability and Quality Control. Proceedings of the International Workshop AMSA’13 (Novosibirsk, September 25-27, 2013), 46–50.
  12. Hoffman I.F., Latkin C.A., Kukhareva P.V., Malov S.V., Batluk J.V., Shaboltas A.V., Skochilov R.V., Sokolov N.V., Verevochkin S.V., Hudgens M.G. & Kozlov A.P. (2013). A Peer-Educator Network HIV Prevention Intervention Among Injection Drug Users: Results of a Randomized Controlled Trial in St. Petersburg, Russia. AIDS and Behavior, Vol. 17, Issue 7, pp 2510-2520.
  13. Dobrynin P., Matyunina E., Malov S.V. & Kozlov A.P. (2013) The Novelty of Human Cancer/Testis Antigen Encoding Genes in Evolution. International Journal of Genomics, Vol.2013, Article ID 105108, 7 pages.
  14. Malov S.V., Shevchenko, A.K. & O’Brien S.J. (2013) Genome associations discovering. Part 1: Statistical methods (in Russian). Komputerniye instrumenti v obrazovanii, v. 5, pp 17 – 32.
  15. Malov S.V., Shevchenko, A.K. & O’Brien S.J. (2013). Genome associations discovering. Part 2: Multiple testing problem, computer tools and applications (in Russian). Komputerniye instrumenti v obrazovanii, v. 6, pp. 3-17
  16. Christoph, G. and Malov S.V. (2012). Asymptotic Properties of Generalized Multivariate Rank Statistics. Accepted to Communications in Statistics: Theory and Methods.
  17. Bagdonavicius V., Malov S.V.&Nikulin M. (2012). Homogeneity Tests for Related Samples Under Censoring, Communications in Statistics: Simulations and Computations 41(6), 764 – 775.
  18. Malov S.V.,Skochilov R.V. &Kozlov A.P. (2010). Estimation of hazard of epidemic by interval censored data. Russian Journal AIDS, Cancer and Public Health, v. 14, № 1(29), 61 – 64. (in Russian)
  19. Christoph, G. and Malov S.V. (2009). On semiparametric estimation in copula models under right censored data, Proceedings of the 6-th St.-Petersburg Workshop on Simulation (Eds. S.M. Ermakov, V.B. Melas and A.N. Pepelyshev)1, 335 – 340.
  20. Berred A and Malov S.V. (2009).Semiparametric Estimation in Copulas with the Same Marginals, Communications in Statistics: Theory and Methods 38(3), 372 – 392.
  21. Bagdonavicius V., Malov, S., Nikulin, M. (2008). Testing of the homogeneity of marginal distributions in copula models, C. R. Acad. Sci. Paris, Ser. I 346, 445–450.
  22. Bagdonavičius, V., Malov, S.V. and Nikulin, M.S. (2006), Semiparametric Regression Estimation in Copula Models, Communications in Statistics: Theory and Methods 35(8), 1449 – 1467.
  23. N. Balakrishnan and S.V. Malov (2005), Some characterizations of exponential distribution based on progressively censored order statistics, In Advances on Models, Characterizations and Applications (Eds., N. Balakrishnan, I.G. Bairamov and O.L. Gebizlioglu), Chapter 6, pp.97-109, Chapman & Hall/CRC Press, New York.
  24. Ahsanullah, M., Malov, S.V. (2005), On Characterizations via Equivalent Distributions Properties of Records. Proceedings of the Fifth St.-Petersburg Workshop on Simulation (Eds. S.M. Ermakov, V.B. Melas and A.N. Pepelyshev), 17-22.
  25. Ahsanullah, M. andMalov, S.V. (2004), On Some Characterizations via Distributional Properties of Records, Journal of Statistical Theory and Applications 3(2), 135-140.
  26. Berred, A. andMalov, S.V. (2004), Semiparametric Estimation in Copulas With the Same Marginals, In Longevity, Aging and Degradation Models in Reliability, Public Health, Medicine and Biology LAD’2004 (eds.,V.Antonov, C.Huber, M.Nikulin, V.Polischook ), pp. 45-51, St.-Petersburg State Politechnical University, St.-Petersburg.
  27. Ahsanullah, M. andMalov, S.V. (2003). On Characterizations via Linear Regression Properties of Generalized Order Statistics. Journal of Statistical Theory and Applications 2(1), 33-38.
  28. Balakrishnan, N., Malov, S.V. (2002) Characterizations of proportional Archimedean copulas. Mathematical Methods of Statistics 11, No 4, 489-495.
  29. Malov, S.V. (2001) On finite-dimensional Archimedean copulas. In Asymptotic Methods in Probability and Statistics with applications (eds.,N.Balakrishnan, I. Ibragimov and V. Nevzorov), Birkhouser, Boston, 19-35,.
  30. Malov, S.V. (2000) On proportional Archimedean copulas. Abstracts of the second international conference on mathematical methods in reliability, Bordeaux, France, v.2, 743-746.
  31. Bagdonavicius V., Malov, S.,Nikulin, M. (1999) Characterizations and semiparametric regression estimation in Archimedean copulas. Journal of Applied Statistical Science 8, No 2/3, 137-154.
  32. Malov, S.V. (1998) Random variables generated by ranks in dependent schemes. Metrika 48, 61-67.
  33. Malov, S.V. (1998) Some remarks on copulas. Abstracts of communications of the conference “Asymptotic Methods in Probability and Mathematical Statistics” in St.-Petersburg, June 24-28, 166-170.
  34. Malov, S.V., Nevzorov, V.B. (1997) Characterizations using ranks and order statistics. In: A Volume in Honour of Samuel Kotz, Wiley, NY., 479-489.
    Malov, S.V. (1997) Sequentialτ-ranks. Journal of Applied Statistical Science 5, No 2/3, 211-224.

  35. Malov, S.V. (1997) Some remarks on finitely dimensional Archimedean copulas. Technical report 97034 of MAB, University Bordeaux 1.
  36. Malov, S.V. (1996) On characterizations of independent identically distributed random variables via order statistics. Statistics & Probability Letters 26, 97-104
  37. Malov, S.V.,Nevzorov, V.B., Nikulin, M.S. (1996) Sequential ranks and related topics. Mathematical Methods in Stochastic, Simulation and Experimental Design (Proceedings of the Second St.-Petersburg Workshop on Simulation, St.-Petersburg 1996), 294-299.
  38. Malov, S.V. (1994) On the strong independence of sequential ranks. Proc. of the Sixth Vilnius Conference in Probab. Th. and Math. Stat. 2, Mokslas Vilnius/VSP, Utrecht, 517-532.
  39. Malov, S.V. (1993) Sequential ranks and order statistics. Notes Sci.Seminars POMI, 204, 115-125 .
  40. Malov, S.V. (1992) On independence of sequential ranks. Vestnik St.-Petersburg Univ. 25, No.3, 109-113

Serguei Simonov

Senior Research Fellow


Serguei A. Simonov, Ph.D., joined the Theodosius Dobzhansky Center for Genome Informatics in November 2012 after conducting genome research projects at Boise (Idaho) State University and at University of North Carolina – Chapel Hill USA.

The focus of his research was in the application of mathematical and computational approaches to genomics for the purpose of interpreting existing data for new gene models with a human health focus. It utilized different techniques including Discrete Fourier Transformation, Formal Grammar, Diophantine Equation Solving and Linear Integer Optimization in application to RNA/DNA and proteomic sequences in a multidisciplinary research approach to bio-informatics. Prior genetics research included working with genomics in development of new techniques for discovering knowledge about RNA/DNA sequence analysis, correlation of RNA/DNA sequences with proteomic data, and solving problems in genetics and related applications.

Dr. Simonov’s scientific interests are in computer science, mathematics and high-performance computing, specifically, theoretical and practical applications of computation, advanced computing, mathematics and applied algorithms in scientific environments, developing new algorithms and it’s computational complexity. He previously held senior research positions at the Russian Academy of Sciences – Siberian Division and the Institute of Computing Mathematics.

Dr. Simonov’s academic background includes teaching undergraduate and graduate courses at universities in Russia (Novosibirsk State University, Novosibirsk State Technical University and Novosibirsk Polytechnic College) and as a visiting professor in Latvia (University of Latvia and Riga Technical University), in addition to supervising students for completion of qualifying scientific work and theses.

Computer science and mathematics are his areas of academic specialty and those in which he holds advanced degrees from the Russian Academy of Science Computing Center and Novosibirsk State University. Dr. Simonov has authored or co-authored more than 30 publications, papers and research and articles in scientific and technical journals, in Russia and internationally, including popular publications, such as PC Week. He is a member of the American Mathematical Society.

Dr. Simonov enjoys all types of outdoor adventure and activities, and is intrigued by new and innovative technologies.

Anna Gorbunova

Senior researcher

Ekaterina Chernyaeva

Ekaterina is a postdoctoral fellow at the Theodosius Dobzhansky Center for Genome Informatics. Ekaterina has graduated from the St.Petersburg State University with aPh.D. in Biology (Biochemistry) in March 2012. Her Ph.D. thesis was devoted to molecular-biological study of Mycobacterium tuberculosis strains spread in St. Petersburg in different patient-groups and analysis of point mutations associated with drug resistance. She started her research work as a student of the University studying genetic diversity of HIV-1 isolates obtained among injecting drug users living in St. Petersburg. This work has been performed within bounds of the Russian HIV/AIDS vaccine development project. In 2006-2007 she attended Advanced Tuberculosis Laboratory Training (Wadsworth Center, New York State Department of Health, USA) funded by Fogarty International Center, NIH. After return to Russia she started to study M. tuberculosis complex strains spread in St. Petersburg and Leningrad region. Her scientific interests lie in the field of molecular biology of human pathogens and human genetic markers associated with infectious diseases.

List of publications

  1. Chernyaeva E, Dobrynin P, Pestova N, Matveeva N, Zhemkov V, Kozlov A. Molecular genetic analysis of Mycobacterium tuberculosis strains spread in different patient groups in St. Petersburg, Russia. Eur J Clin Microbiol Infect Dis. 2012 Aug;31(8):1753-7. doi: 10.1007/s10096-011-1497-2. Epub 2011 Dec 8. PubMed PMID: 22160887.
  2. Chernyaeva E, Fedorova E, Zhemkova G, Korneev Y, Kozlov A. Characterization of multiple and extensively drug resistant Mycobacterium tuberculosis isolates with different ofloxacin-resistance levels. Tuberculosis (Edinb). 2013 May;93(3):291-5. doi: 10.1016/j.tube.2013.02.005. Epub 2013 Mar 13. PubMed PMID: 23491718.
  3. Chernyaeva EN, Shulgina MV, Rotkevich MS, Dobrynin PV, Simonov SA, Shitikov EA, Ischenko DS, Karpova IY, Kostryukova ES, Ilina EN, Govorun VM, Zhuravlev VY, Manicheva OA, Yablonsky PK, Isaeva YD, Nosova EY, Mokrousov IV, Vyazovaya AA, Narvskaya OV, Lapidus AL, O’Brien SJ. Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology. BMC Genomics. 2014 Apr 25;15:308. doi: 10.1186/1471-2164-15-308. PubMed PMID: 24767249; PubMed Central PMCID: PMC4234438.
  4. Zimenkov DV, Kulagina EV, Antonova OV, Krasnova MA, Chernyaeva EN, Zhuravlev VY, Kuz’min AV, Popov SA, Zasedatelev AS, Gryadunov DA. Evaluation of a low-density hydrogel microarray technique for mycobacterial species identification. J Clin Microbiol. 2015 Apr;53(4):1103-14. doi: 10.1128/JCM.02579-14. Epub 2015 Jan 21. PubMed PMID: 25609722; PubMed Central PMCID: PMC4365248.
  5. Acosta F, Chernyaeva E, Mendoza L, Sambrano D, Correa R, Rotkevich M, Tarté M, Hernández H, Velazco B, de Escobar C, de Waard JH, Goodridge A. Mycobacterium bovis in Panama, 2013. Emerg Infect Dis. 2015 Jun;21(6). doi: 10.3201/eid2106.141821. PubMed PMID: 25988479.
  6. Velichko N, Chernyaeva E, Averina S, Gavrilova O, Lapidus A, Pinevich A. Consortium of the ‘bichlorophyllous’ cyanobacterium Prochlorothrix hollandica and chemoheterotrophic partner bacteria: culture and metagenome based description. Environ Microbiol Rep. 2015 May 20. doi: 10.1111/1758-2229.12298. [Epub ahead of print] PubMed PMID: 25990300.
  7. И. В. Духовлинов, Е. А. Федорова, Е. Г. Богомолова, О. А. Добровольская, Е. Н. Черняева, Р. И. Аль-Шехадат, А. С. Симбирцев. ПОЛУЧЕНИЕ РЕКОМБИНАНТНОГО БЕЛКА CRM197 В КЛЕТКАХ E. COLI. Инфекция и иммунитет 2015, Т. 5, No 1, с. 37–44
    DOI: http://dx.doi.org/10.15789/2220-7619-2015-1-37-44
  8. Trends in molecular epidemiology of drug-resistant tuberculosis in Republic of Karelia, Russian Federation
    Igor Mokrousov, Anna Vyazovaya, Natalia Solovieva, Tatiana Sunchalina, Yuri Markelov, Ekaterina Chernyaeva, Natalia Melnikova, Marine Dogonadze, Daria Starkova, Neliya Vasilieva, Alena Gerasimova, Yulia Kononenko, Viacheslav Zhuravlev, Olga Narvskaya
    BMC Microbiol. 2015; 15: 279. Published online 2015 December 18. doi: 10.1186/s12866-015-0613-3
    PMCID: PMC4683759
  9. Suvorov A, Dukhovlinov I, Leontieva G, Kramskaya T, Koroleva I, Grabovskaya K, Fedorova E, Chernyaeva E, Klimov N, Orlov A and Uversky V
    Chimeric Protein PSPF, a Potential Vaccine for Prevention Streptococcus pneumoniae Infection
    J Vaccines Vaccin 6:304. doi:10.4172/2157-7560.1000304
  10. Chernyaeva E. Biochemical mechanisms of Mycobacterium tuberculosis drug resistance // Vestnik St. Petersburg University. Ser. 3. 2012. Issue 2. P. 77–91.
  11. Chernyaeva E, Dobrynin P, Pestova N, Matveeva N, Zhemkov V, Kozlov. A. / Evaluation of mutations in gyrA and gyrB genes associated with ofloxacin-resistance and molecular-genetic characteristic of ofloxacin-resistant M. tuberculosis isolates revealed in St. Petersburg in 2008. // Vestnik St. Petersburg University, 2010. Series 3, V.4. P. 117-125
  12. E. Chernyaeva, A. Masharsky, S. Verevochkin, S. Gagarina, N. Klimov, A. Kozlov / Genetic Diversity of HIV-1 isolates Spread Among Injecting Drug Users in St. Petersburg // Physiology and Pathology of Immune System, 2007. V.11, №2, P. 9-14.

Klaus-Peter Koepfli

My primary research interests are in evolutionary genomics, conservation genetics, and molecular ecology.

I use genetic and genomic methods to understand the patterns and processes of divergence among genes, populations, and species. Through the Genome 10K project, I am currently involved in projects using next-generation sequencing technologies and comparative genomics to generate and analyze genomes across the vertebrate tree of life. I also use bioinformatic approaches to assemble and analyze phylogenomic data sets to test phylogenetic hypotheses and understand how variation in functional constraint can affect phylogenetic signal and gene tree/species tree reconstruction. I am especially interested in the molecular evolution of the mammalian order Carnivora (dogs, cats, bears and their kin) and my research uses population genetic and phylogenetic tools to elucidate the evolutionary history within and among carnivoran species in the context of paleoenvironmental history.

My research also involves using molecular methods to address important issues in the conservation and management of biodiversity. This involves assessing the amount and distribution of genomic variation within populations using next-generation sequencing technologies, developing tools to enhance understanding of the abundance and distribution of species across their habitats, and using integrative data sets and species delimitation methods to confirm or update taxonomies.

Nikolai Cherkasov

Chief Specialist

One of the key person in the center who from the very beginning support all information infrastructure of the lab’s activities, including servers support, technical equipment and software support