Source: http://rcpcm.org/scientific-research/molecular-biology-and-genetics/bioinformatics/
Timestamp: 2019-04-23 10:22:09+00:00

Document:
Bioinformatics laboratory was created in 2013. We are a team of highly qualified young scientists, bioinformaticians, students and graduates of the best universities in the country. We apply our skills and knowledge in bioinformatics and statistical analysis to various types of biological data (usually of clinical importance). We participate in international and local conferences, as well as in international research projects. We are organizing bioinformatics schools. Since 2010, we are taking part in the Russian Metagenome project.
Conducting intensive calculations on a computing cluster of our institute.
Hobbies: coding, hackathons, hiking, travelling, art house, philosophy, video games, cinema club, science fiction literature.
Metagenomics of human intestinal microbiota. Analysis of data from next-generation sequencers, including ABI SOLiD. Phylogenetic and functional description, statistical analysis of socio-geographic and medical groups, metabolic reconstruction, search for functional markers. Participation in the Russian Metagenome project (http://www.metagenome.ru).
Biological data visualization bringing about generation and validation of biological hypotheses.
Bacterial genomics: obtaining bacterial genomes on the basis of next-generation sequencing (NGS) data; annotation. The subjects of our genome projects include the Mollicutes (Spiroplasma melliferum, Acholeplasma laidlawii, Mycoplasma gallisepticum) and Helicobacter pylori.
Resequencing of human genome on next-generation sequencers; risk prediction for development of pathological processes using polymorphisms and structural rearrangements; analysis of a personal genetic profile.
3. Complete genome and proteome of Acholeplasma laidlawii. Lazarev VN, Levitskii SA, Basovskii YI, Chukin MM, Akopian TA, Vereshchagin VV, Kostrjukova ES, Kovaleva GY, Kazanov MD, Malko DB, Vitreschak AG, Sernova NV, Gelfand MS, Demina IA, Serebryakova MV, Galyamina MA, Vtyurin NN, Rogov SI, Alexeev DG, Ladygina VG, Govorun VM. J Bacteriol. 2011 Sep;193(18):4943-53. Epub 2011 Jul 22.
4. Core proteome of the minimal cell: comparative proteomics of three mollicute species. Fisunov GY, Alexeev DG, Bazaleev NA, Ladygina VG, Galyamina MA, Kondratov IG, Zhukova NA, Serebryakova MV, Demina IA, Govorun VM. PLoS One. 2011;6(7):e21964. Epub 2011 Jul 19.
5. New method for peptide desorption from abundant blood proteins for plasma/serum peptidome analyses by mass spectrometry. Ziganshin R, Arapidi G, Azarkin I, Zaryadieva E, Alexeev D, Govorun V, Ivanov V. J Proteomics. 2011 May 1;74(5):595-606. Epub 2011 Feb 2.
6. Comparative proteomic characteristic of Mycoplasmas (Mollycutes). Demina IA, Serebriakova MV, Ladygina VG, Galiamina MA, Zhukova NA, Alekseev DG, Fisunov GIu, Govorun VM. Bioorg Khim. 2011 Jan-Feb;37(1):70-80. Russian.
7. Functional divergence of Helicobacter pylori related to early gastric cancer. Momynaliev KT, Kashin SV, Chelysheva VV, Selezneva OV, Demina IA, Serebryakova MV, Alexeev D, Ivanisenko VA, Aman E, Govorun VM. J Proteome Res. 2010 Jan;9(1):254-67.
8. Complete genome and proteome of Acholeplasma laidlawii. Lazarev VN, Levitskii SA, Basovskii YI, Chukin MM, Akopian TA, Vereshchagin VV, Kostrjukova ES, Kovaleva GY, Kazanov MD, Malko DB, Vitreschak AG, Sernova NV, Gelfand MS, Demina IA, Serebryakova MV, Galyamina MA, Vtyurin NN, Rogov SI, Alexeev DG, Ladygina VG, Govorun VM. J Bacteriol. 2011 Sep;193(18):4943-53. Epub 2011 Jul 22.
9. Serum proteome profiling for ovarion cancer diagnosis using ClinProt magnetic bead technique and MALDI-TOF-mass-spectrometry. Ziganshin RKh, Alekseev DG, Arapidi GP, Ivanov VT, Moshkovskiĭ SA, Govorun VM. Biomed Khim. 2008 Jul-Aug;54(4):408-19. Russian.
13. Zgoda, Victor G., Arthur T. Kopylov, Olga V. Tikhonova, Alexander A. Moisa, Nadezhda V. Pyndyk, Tatyana E. Farafonova, Svetlana E. Novikova, Andrey V. Lisitsa, Elena A. Ponomarenko, Ekaterina V. Poverennaya, Sergey P. Radko, Svetlana A. Khmeleva, Leonid K. Kurbatov, Aleksey D. Filimonov, Nadezhda A. Bogolyubova, Ekaterina V. Ilgisonis, Aleksey L. Chernobrovkin, Alexis S. Ivanov, Alexei E. Medvedev, Yury V. Mezentsev, Sergei A. Moshkovskii, Stanislav N. Naryzhny, Elena N. Ilina, Elena S. Kostryukova, Dmitry G. Alexeev, Alexander V. Tyakht, Vadim M. Govorun, and Alexander I. Archakov. "Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells." Journal of proteome research 12, no. 1 (2012): 123-134.
17. Gorbachev Y Alexey, Fisunov Y Gleb, Izraelson Mark, Evsyutina V Darya, Mazin V Pavel, Alexeev G Dmitry, Pobeguts V Olga, Gorshkova N Tatyana, Kovalchuk I Sergey, Kamashev E Dmitry, Govorun M Vadim, DNA repair in Mycoplasma gallisepticum, BMC Genomics.2013, 14:726.
19. Ponomarenko EA, Kopylov AT, Lisitsa AV, Radko SP, Kiseleva YY, Kurbatov LK,Ptitsyn KG, Tikhonova OV, Moisa AA, Novikova SE, Poverennaya EV, Ilgisonis EV,Filimonov AD, Bogolubova NA, Averchuk VV, Karalkin PA, Vakhrushev IV, Yarygin KN,Moshkovskii SA, Zgoda VG, Sokolov AS, Mazur AM, Prokhortchouck EB, Skryabin KG,Ilina EN, Kostrjukova ES, Alexeev DG, Tyakht AV, Gorbachev AY, Govorun VM,Archakov AI. Chromosome 18 transcriptoproteome of liver tissue and HepG2 cellsand targeted proteome mapping in depleted plasma: update 2013. J Proteome Res.2014 Jan 3;13(1):183-90. doi: 10.1021/pr400883x. Epub 2013 Dec 13. PubMed PMID:24328317.
20. Shitikov EA, Bespyatykh JA, Ischenko DS, Alexeev DG, Karpova IY, KostryukovaES, Isaeva YD, Nosova EY, Mokrousov IV, Vyazovaya AA, Narvskaya OV, VishnevskyBI, Otten TF, Zhuravlev VY, Yablonsky PK, Ilina EN, Govorun VM. Unusuallarge-scale chromosomal rearrangements in Mycobacterium tuberculosis BeijingB0/W148 cluster isolates. PLoS One. 2014 Jan 8;9(1):e84971. doi:10.1371/journal.pone.0084971. eCollection 2014. PubMed PMID: 24416324; PubMedCentral PMCID: PMC3885621.
21. Tyakht AV, Alexeev DG, Popenko AS, Govorun VM. Rural and urban microbiota: To be or not to be? Gut Microbes. 2014 Apr 1;5(3). [Epub ahead of print] PubMedPMID: 24691073.
22. Ahmetov II, Naumov VA, Donnikov AE, Maciejewska-Karłowska A, Kostryukova ES,Larin AK, Maykova EV, Alexeev DG, Fedotovskaya ON, Generozov EV, Jastrzębski Z,Zmijewski P, Kravtsova OA, Kulemin NA, Leonska-Duniec A, Martykanova DS, OspanovaEA, Pavlenko AV, Podol'skaya AA, Sawczuk M, Alimova FK, Trofimov DY, Govorun VM, Cieszczyk P. SOD2 gene polymorphism and muscle damage markers in elite athletes. Free Radic Res. 2014 Aug;48(8):948-55. doi: 10.3109/10715762.2014.928410. Epub2014 Jun 23. PubMed PMID: 24865797.
23. Mustafina LJ, Naumov VA, Cieszczyk P, Popov DV, Lyubaeva EV, Kostryukova ES,Fedotovskaya ON, Druzhevskaya AM, Astratenkova IV, Glotov AS, Alexeev DG,Mustafina MM, Egorova ES, Maciejewska-Karłowska A, Larin AK, Generozov EV,Nurullin RE, Jastrzębski Z, Kulemin NA, Ospanova EA, Pavlenko AV, Sawczuk M,Akimov EB, Danilushkina AA, Zmijewski P, Vinogradova OL, Govorun VM, Ahmetov II. AGTR2 gene polymorphism is associated with muscle fibre composition, athleticstatus and aerobic performance. Exp Physiol. 2014 May 30. [Epub ahead of print]PubMed PMID: 24887114.

References: V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V.