Research Project Portals

Vladimir Brukhin    

Leading researcher, Deputy Director 

Joined the Theodosius Dobzhansky Center for Genome Bioinformatics in February 2013 right 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 Genome Russia project (http://genomerussia.bio.spbu.ru/?lang=en), main goal of which is the creation of 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:

  • Zhernakova DV, Brukhin V, Malov S, Oleksyk TK, Koepfli KP, Zhuk A, Dobrynin P, Kliver S, Cherkasov N, Tamazian G, Rotkevich M, Krasheninnikova K, Evsyukov I, Sidorov S, Gorbunova A, Chernyaeva E, Shevchenko A, Kolchanova S, Komissarov A, Simonov S, Antonik A, Logachev A, Polev DE, Pavlova OA, Glotov AS, Ulantsev V, Noskova E, Davydova TK, Sivtseva TM, Limborska S, Balanovsky O, Osakovsky V, Novozhilov A, Puzyrev V, O'Brien SJ. Genomics. 2019 Mar 19. pii: S0888-7543(18)30741-9. doi: 10.1016/j.ygeno.2019.03.007. PMID: 30902755
  • Brukhin V, Osadtchiy JV, Florez-Rueda AM, Smetanin D, Bakin E, Nobre MS and Grossniklaus U (2019) The Boechera Genus as a Resource for Apomixis Research. Front. Plant Sci. 10:392. doi: 10.3389/fpls.2019.00392
  • Brukhin V., Baskar R. (2019) Evolutionary and ecological role of apomixis and asexual reproduction. The International Journal of Plant Reproductive Biology. 11(1), pp.70-83. doi: 10.14787/ijprb.2019 11.1.
  • Brukhin V., Baskar R. A brief note on genes that trigger components of apomixis (2019). Journal of Biosciences, 44:45. https://doi.org/10.1007/s12038-019-9850-1
  • Kliver S., Rayko M., Komissarov A., Bakin E., Zhernakova D., Prasad K., Rushworth C., Baskar R., Smetanin D1., Schmutz J., Rokhsar D/S., Mitchell-Olds T., Grossniklaus U., Brukhin V. (2018) Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes. Genes (Basel). 28;9(4). doi: 10.3390/genes9040185.
  • 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.
  • Osadtchiy J. V., Naumova T. N., Brukhin V. B. (2017) APOMIXIS IN THE GENUS BOECHERA (BRASSICACEAE). Bot. J. 102 (12): 1587-1607.
  • Brukhin V. (2017) Molecular and Genetic Regulation of Apomixis. Russian Journal of Genetics 53(9):1001-1024. doi: 10.1134/S1022795417090046
  • 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
  • Oleksyk TK, Brukhin V, O’Brien SJ. (2015) Putting Russia on the genome map. Science. 13; 350 (6262): 747.
  • 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.
  • 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.
  • 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
  • Brukhin V. and Morozova N. (2011) Plant growth and development – basic knowledge and current views. Mathematical Modelling Natural Phenomena, 6 (2): 1- 53.
  • 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. 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.
  • 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.
  • Brukhin V., Curtis M.D., Grossniklaus U. (2005) The angiosperm female gametophyte: no longer forgotten generation. Review Current Science, 89 (11).
  • 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.
  • 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.
  • 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.
  • 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.
  • 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. 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. 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.
  • 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. 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.
  • 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.
  • 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.
  • 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.

RESEARCH PROJECTS OF THE CENTER

Genome Russia Project

Genes are the basic “instruction book” for the cells that make up our bodies, and are made out of DNA. The DNA of a person is more than 99% the same as the DNA of any other unrelated person. But no two people have exactly the same DNA except identical twins. Differences in DNA are called genetic variations. They explain some of the physical differences among people, and partly explain why some people get diseases like cancer, diabetes, asthma, and depression, while others do not. Such diseases may also be affected by factors like diet, exercise, smoking, and pollution in the environment, which makes it hard to figure out which genes affect the diseases.

GWATCH - web-based genome browser for genome-wide association studies

GWATCH is a web-based genome browser designed to automate analysis, visualization and release of data from genome-wide association studies (GWAS) and whole genome sequence association studies of genetic epidemiological cohorts. For any association study, GWATCH allows cataloging and viewing of significant statistical results of association tests (p-values, odds ratios, hazard ratios and others) for single or multiple variants (SNP, indels, CNV), for single or multiple tests.

Genome-based Mycobacterium Tuberculosis Variation Database

Comparative genomics of Mycobacterium tuberculosis clinical strains spread in Russia – is one of the research projects conducted at Theodosius Dobzhansky Center for Genome Bioinformatics. We are studying genomic signatures associated with M. tuberculosis clinical and microbiological features. A Database of M. tuberculosis Genome Variations (GMTV) developed by our team, integrates clinical, epidemiological and microbiological information with genome variations based on whole genome sequencing data. This research is conducted in collaboration with St. Petersburg Research institute of Phthisiopulmonology and St. Petersburg Pasteur Institute, and supported by St. Petersburg State University and Russian Foundation for Basic Research (RFBR) grants.

Single-cell analysis of tumor-microenvironment interactions in follicular lymphoma

Follicular lymphoma

Follicular Lymphoma (FL) is a slow-growing cancer of the lymphatic system, which affects one in every three thousand individuals. While existing frontline therapies are effective at suppressing FL, it remains an incurable disease with a median survival of 8-10 years. A fifth of the patients develop resistance to the standard treatment within the first two years. Understanding the mechanisms facilitating resistance and identifying early molecular prognostic indicators remains a high priority.

Assembly, Annotation, and Comparative Analysis of Apomictic Boechera Species Genome

Principal investigator of the project Vladimir Brukhin

Apomixis is asexual way of plant reproduction through seeds, which could be found in more than 400 plant species representing almost 40 families. It is believed that apomixis evolved independently in several taxa from sexual ancestors. Apomixis could be considered as a developmental variation of sexual reproduction in which some steps are lost, reduced, deregulated or desynchronized (Fig.1). The main features of gametophytic apomixis are:

  • Avoidance of meiosis (apomeiosis);
  • Embryo formation via parthenogenesis;
  • Functional endosperm develops either autonomously or pseudogamously (central cell fertilized by sperm cell).

Theodosius Dobzhansky

Geneticist & Evolutionary Biologist
 
Theodosius Dobzhansky American geneticist and evolutionary biologist and a central figure in the field of evolutionary biology is recognized for...

Stephen J O'Brien

Chief Scientific Officer
 
I welcome you to the Site of the brand new Center of Genome Informatics at St Petersburg State University. The...

Vladimir Brukhin

Leading researcher, Deputy Director 
 
Vladimir Brukhin    Leading researcher, Deputy Director  Joined the Theodosius Dobzhansky Center for Genome Bioinformatics in February 2013 right after returning...

Lab's news

SPBU on web site published an article about achievement of the Center and published article.

Wednesday 10.07.2019 at 3pm. Alexander Tiskin (Department of Computer Science, University of Warwick, United Kingdom) "The surprising algebra of sequence alignment".