Lab of Bioinformatics

About the Laboratory

About the Laboratory

Bioinformatics Laboratory, 2013 Слева направо: Борис Коварский, Александр Манолов, Александр Тяхт, Анна Попенко, Илья Алтухов, Николай Кулемин, Александр Павленко, Дмитрий Ищенко, Дмитрий Алексеев, Павел Мазин, Владимир Наумов, Александр Зеленин
Bioinformatics Laboratory, 2013
Left to right: Boris Kovarsky, Alexander Manolov, Alexander Tyakht, Anna Popenko, Ilya Altukhov, Nikolay Kulemin, Alexander Pavlenko, Dmitry Ischenko, Dmitry Alexeev, Pavel Mazin, Vladimir Naumov, Alexander Zelenin

We are the “youngest” laboratory in SRI PCM, founded in 2008. Despite this, we are an excellent team of graduates from the best Russian higher education institutions. We are passionate about science. This passion unites us and drives us to tackle all problems related to our scientific activities, ranging from cabling and a repair of a computer to multicomponent analysis of intestinal microbiota. And if this somehow relates to biology and computers, we call it Bioinformatics.

Our profile is genomic, transcriptomic, and proteomic studies, the analysis of data that are the results of sequencing and mass-spectrometric analysis, and the building of models of biological systems. Not least important for us are methods of statistical treatment of data, namely multiparametric tests used for large cohorts.
From 2010, we are actively participating in the Russian Metagenome project - metagenome.ru

Considering that the field of bioinformatics by itself is very new among “-omics”, we exert best efforts to organize educational workshops. We deliver a course of lectures on Introduction into Bioinformatics in SRI PCM and MPTI.

Our skills

  • Development of databases and cloud computing for large-scale bioinformatics data sets.
  • Programming in C/C++, C#, Python, Perl.
  • Statistical analysis in R.

We are reading

People

People

Dmitry Alexeev
Ilya Altukhov
Alexander Zelenin
Dmitry Ischenko
Boris Kovarsky
Pavel Mazin
Alexander Manolov
Alexander Pavlenko
Anna Popenko
Ilya Rusalovsky
Alexander Tyakht
Eleonora Khlebus
Tatyana Shashkova

Projects of the laboratory

Projects of the laboratory

  • 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.

Publications and conferences

Publications and conferences

Publications

1. Cyto-Insectotoxin 1a from Lachesana tarabaevi Spider Venom Inhibits Chlamydia trachomatis Infection, Nadezhda F. Polina, Marina M. Shkarupeta, Anna S. Popenko, Alexander A. Vassilevski, Sergey A. Kozlov, Eugene V. Grishin, Vassili N. Lazarev, Vadim M. Govorun, Probiotics & Antimicro. Prot. (2012) 4:208–216, DOI 10.1007/s12602-012-9108-9

2. The application of Spiroplasma melliferum proteogenomic profiling for the discovery of virulence factors and pathogenicity mechanisms in host-associated spiroplasmas J. Proteome Res., DOI: 10.1021/pr2008626 Publication Date (Web): November 30, 201Dmitry Alexeev , Elena Kostrjukova , Alexander Aliper , Anna Popenko , Nikolay Bazaleev , Alexander Tyakht , Oksana Selezneva , Tatyana Akopian , Elena Prichodko , Ilya Kondratov , Mikhail Chukin , Irina Demina , Maria Galyamina , Dmitri Kamashev , Anna Vanyushkina , Valentina Ladygina , Sergei Levitskii , Vasily Lazarev and Vadim Govorun

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.

10. Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, Pavlenko AS, Larin AK, Karpova IY, Selezneva OV, Semashko TA, Ospanova EA, Babenko VV, Maev IV, Cheremushkin SV, Kucheryavy YA, Shcherbakov PL, Grinevich VB, Efimov OI, Sas EI, Abdulkhakov RA, Abdulkhakov SA, Lyalyukova EA, Livzan EA, Vlassov VV, Sagdeev RZ, Tsukanov VV, Osipenko MF, Kozlova IV, Tkachev AV, Sergienko VI, Alexeev DG., Govorun V.M., Human gut microbiota compositions found across urban and rural populations of Russia. Nature Communications 2013, doi:10.1038/ncomms3469

11. Alexander V Tyakht1, Anna S Popenko, Maxim S Belenikin, Ilya A Altukhov, Alexander V Pavlenko, Elena S Kostryukova, Oksana V Selezneva, Andrei K Larin, Irina Y Karpova and Dmitry G Alexeev, MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads. Source Code for Biology and Medicine 2012, 7:13 doi:10.1186/1751-0473-7-13

12. ПОТЕНЦИАЛЬНЫЕ ВОЗМОЖНОСТИ ИСПОЛЬЗОВАНИЯ РАСПРЕДЕЛЕННЫХ ВЫЧИСЛИТЕЛЬНЫХ СИСТЕМ ПРИ РЕШЕНИИ КОНЦЕПТУАЛЬНЫХ ПРОБЛЕМ ПОСТРОЕНИЯ ИНФОРМАЦИОННЫХ КОМПЛЕКСОВ ОБРАБОТКИ ДАННЫХ ВЫСОКОПРОИЗВОДИТЕЛЬНОГО ГЕНОМНОГО СЕКВЕНИРОВАНИЯ И ГЛУБОКОГО ПРОТЕОМНОГО ПРОФИЛИРОВАНИЯ. Д.Г. Алексеев, Е.С. Кострюкова, А.С. Попенко, И.В. Русаловский, А.В. Тяхт. Информатизация и связь, 8 (2012)

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.

14. D.D. Kharlampieva, V.A. Manuvera, O.V. Podgorny, S.I. Kovalchuk, O.V. Pobeguts, I.A. Altukhov, D.G. Alexeev, V.N. Lazarev, V.M. Govorun, Purification and characterisation of recombinant Bacteroides fragilis toxin-2, Biochimie 95 (2013) 2123-2131

15. Tatiana V. Grigoryeva, Aleksandr V. Laikov, Rimma P. Naumova, Aleksandr I. Manolov, Andrey K. Larin, Irina Y. Karpova, Tatiana A. Semashko, Dmitry G. Alexeev, Elena S. Kostryukova, Rudolf Müllerd, Vadim M. Govorun, Draft genome of the nitrogen-fixing bacterium Pseudomonas stutzeri strain KOS6 isolated from industrial hydrocarbon sludge, doi: 10.1128/genomeA.00072-12 Genome Announc. January/February 2013 vol. 1 no. 1 e00072-12

16. Elena N Ilina, Egor A Shitikov, Larisa N Ikryannikova, Dmitry G Alekseev, Dmitri E Kamashev, Maja V Malakhova, Tatjana V Parfenova, Maxim V Afanas’ev, Dmitry S Ischenko, Nikolai A Bazaleev, Tatjana G Smirnova, Elena E Larionova, Larisa N Chernousova, Alexey V Beletsky, Andrei V Mardanov, Nikolai V Ravin, Konstantin G Skryabin, Vadim M Govorun, Comparative Genomic Analysis of Mycobacterium tuberculosis Drug Resistant Strains from Russia, PLoS ONE 8(2):e56577. doi:10.1371/journal.pone.0056577

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.

18. Irina V Prokhorova, Ilya A Osterman, Dmitry E Burakovsky, Marina V Serebryakova, Maria A Galyamina, Olga V Pobeguts, Ilya Altukhov, Sergey Kovalchuk, Dmitry G Alexeev, Vadim M Govorun, Alexey A Bogdanov, Petr V Sergiev, Olga A Dontsova, Modified nucleotides m2G966/m5C967 of Escherichia coli 16S rRNA are required for attenuation of tryptophan operon, Nature Scientific Reports, 3, 3236 doi:10.1038/srep03236

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.

24. Eugene E. Kulikov, Alla K. Golomidova, Maria A. Letarova, Elena S. Kostryukova, Alexandr S. Zelenin, Nikolai S. Prokhorov and Andrey V. Letarov, Genomic Sequencing and Biological Characteristics of a Novel Escherichia Coli Bacteriophage 9g, a Putative Representative of a New Siphoviridae Genus, Viruses 2014, 6(12), 5077-5092; doi:10.3390/v6125077

25. Igor A Fesenko, Georgij P Arapidi, Alexander Y Skripnikov, Dmitry G Alexeev, Elena S Kostryukova, Alexander I Manolov, Ilya A Altukhov, Regina A Khazigaleeva, Anna V Seredina, Sergey I Kovalchuk, Rustam H Ziganshin, Viktor G Zgoda, Svetlana E Novikova, Tatiana A Semashko, Darya K Slizhikova, Vasilij V Ptushenko, Alexey Gorbachev, Vadim M Govorun, Vadim T Ivanov, Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens, BMC Plant Biology 2015, 15:87, doi:10.1186/s12870-015-0468-7

Conferences

1. Explanation of Helicobacter Pylori Virulence and Adaptation Based on Proteogenomic Analysis. Dmitry Alexeev, Russian Institute Of Physico-Chemical Medicine, Moscow, RU. ISCB Symposium 2011.

2. Core proteome of Helicobacter pylori strains deduced from proteogenomic comparsion between laboratory strains and clinical isolate sheds light on possible evolution and adaptation of virulence mechanisms. Dmitry Alexeev. HUPO 2011 World Congress.

3. Web-application for comparative structural and functional analysis of prokaryotic genomes sequencing data. Ilya Altukhov. MCCMB'11.

4. Temporal evolution of gut microbiota during chemotherapy in acute leukemia pediatric patients. Tyakht A.V., Popenko A.S., Zelenin A.S., Kovarsky B.A., Alexeev D.G., Karpova I.Y., Larin A.K., Solopova G.G., Dzhandarova D.T., Roumiantsev S.A., Kostryukova E.S., International Human Microbiome Congress (IHMC), Hangzhou, 2013.

5. Peskov, K., Kosinsky, Y., Popenko, A., Tyakht, A., & Alexeev, D. (2012, September). Mechanistic modeling approach relating human gut microbial community to physiologically-relevant biomarkers. In SYSPATHO WORKSHOP SYSTEMS BIOLOGY AND MEDICINE (p. 53).

6. Метагеномный анализ микробиоты населения РФ. Тяхт А.В., Попенко А.С., Беленикин М.С., Павленко А.В., Алексеев Д.Г. III международная научно-практическая конференция "Постгеномные методы анализа в биологии, лабораторной и клинической медицине", Казань, 2012.

7. И.А. Алтухов «Количественная безметочная протеомика и системный анализ штаммов Helicobacter pylori», Конференция молодых ученых НИИ ФХМ, Москва, 2013

8. Д.С. Ищенко "Разработка программного комплекса для анализа бактериальных данных", Конференция молодых ученых НИИ ФХМ, Москва, 2013

9. И.А. Алтухов, Д.С. Ищенко, Ковальчук С.И. и Д.Г. Алексеев, «Количественная безметочная протеомика и системны анализ штаммов Helicobacter pylori», Международная научная школа для молодёжи и преподавателей «Прикладные математика и физика: от фундаментальных исследований к инновациям»", Москва, 2013

10. И.А. Алтухов «Сравнительный геномный анализ штаммов Helicobacter pylori и Neisseria gonorrhoeae». Международная конференция "Высокопроизводительное секвенирование в геномике", Новосибирск, 2013

11. Д.С. Ищенко «Толерантность протеомных данных». Х студенческая конференция факультета биоинженерии и биоинформатики МГУ, Москва, 2013

12. А.С. Зеленин "Структура бактериального сообщества пищеварительного тракта криптобиотической хирономиды Polypedilum vanderplanki с позиции метагеномного анализа". Международная конференция «Высокопроизводительное секвенирование в геномике», Новосибирск, 2013

13. Б.А. Коварский, Д.Г. Алексеев, Анализ генетического разнообразия в метагеноме кишечника человека. Конференция молодых ученых НИИ ФХМ, Москва, 2013

14. Б.А. Коварский, А.С. Попенко, А.В. Тяхт, П. Мазин, Д.Г. Алексеев «Анализ генетической изменчивости кишечной микробиоты человека». Международная конференция «Высокопроизводительное секвенирование в геномике», Новосибирск, 2013

15. А.С. Попенко, А.В. Тяхт, Д.Г. Алесеев «Особенности микробиоты кишечника российской популяции: функциональный анализ и межнациональное сравнение.», Международная конференция «Высокопроизводительное секвенирование в геномике», Новосибирск, 2013

16. А.В. Тяхт «Метагеномное исследование временной эволюции состава микробиоты кишечника в ходе курса противораковой терапии у детей». Международная конференция «Высокопроизводительное секвенирование в геномике», Новосибирск, 2013

17. Tyakht A.V., Popenko A.S., Zelenin A.S., Kovarsky B.A., Alexeev D.G., Karpova I.Y., Larin A.K., Solopova G.G., Dzhandarova D.T., Roumiantsev S.A., Kostryukova E.S. «Temporal evolution of gut microbiota during chemotherapy in acute leukemia pediatric patients». International Human Microbiome Congress (IHMC), Hangzhou, 2013

18. А.И. Манолов «Сборка de-novo и сравнительный анализ бактерии P. stutzeri KOS6, извлеченной из нефтяного шламма». Международная конференция «Высокопроизводительное секвенирование в геномике», Новосибирск, 2013

19. Yuri Kosinsky, Kirill Peskov, Anna Popenko, Aleksndr Tyakht,, Dmitry Alexeev «Modeling of short-chain fatty acids metabolism in human gut: reconstruction of possible relations between microbiota composition and type 2 diabetes status». FEBS, Saint-Petersburg, 2013

20. Dmitry Alexeev « Systems biology of h. pylori». FEBS, Saint-Petersburg, 2013

21. Дмитрий Алексеев, «Системная биология H.pylori» Белки и пептиды, Уфа, 2013

22. Дмитрий Алексеев, «Становление микробиоты младенца» Мать и дитя, Москва, 2013

23. Дмитрий Алексеев, «Оценка резервуара биомаркеров» Трансляционная медицина Москва, 2013

24. Дмитрий Алексеев, «Генмный анализ хирономиды» Международная конференция «Высокопроизводительное секвенирование в геномике», Новосибирск, 2013