Laboratory of Big Data Analysis for Digital Pharmacology
|
CONTACTS |
|
|
|
|
|
|
||
|
Andrei A. Kashirin
|
Viktoria M. Lusina
|
The laboratory was established in 2024 for the purpose of studies within the framework of the research "Big data analysis of medical virology for the search of effective and safe antiviral compounds and optimization of therapy of infectious diseases" supported by the Program of Basic Scientific Research in the Russian Federation for the long-term period (2021-2030) (№124050800018-9).
THE PURPOSES OF THE LABORATORY
THE MAIN DIRECTIONS OF RESEARCH
Development of computer methods and software tools for automated extraction, integration and analysis of large chemical and biomedical data. The methods for extraction, integration and analysis of biomedical data are based on the application of machine learning methods.
- Development of a data organisation scheme within the system "Chemical сompound - molecular target - pharmacological and toxic cffects - disease".
- To develop and improve algorithms to analyse text data and automatically extract associations between objects (biological and chemical molecules).
- Compilation of training sets and building of machine learning models to estimate the effects of antiviral compounds, including side effects and toxicity.
- Development and improvement of algorithms for network analysis of intermolecular interactions for a comprehensive understanding of the mechanisms of side effects and toxicity of pharmacologically active antiviral compounds.
- Development of an information and computing platform for data selection of known effects of antiviral compounds and computational prediction of pharmacological, adverse and toxic effects.
The head of the laboratory, O.A. Tarasova, PhD is the author/co-author of more than forty articles, 38 are indexed by Web of Science Core Collection (WoS H-index 13), 40 are indexed by Scopus (Scopus h-index 14); more than 70 scientific papers indexed by RSCI (RSCI h-index 12). In 2024 O.A. Tarasova was awarded the Prize for the best scientific work of the first degree at the Forum of Young Scientists dedicated to the 300th anniversary of the Russian Academy of Sciences and the 80th anniversary of the Academy of Medical Sciences of the USSR (RAMS) "Medical Science: yesterday, today, tomorrow". The prize was awarded for the study "Analysis of HIV-host interaction using bioinformatics methods" in the section "Innovative methods and technologies".
O.A. Tarasova in 2016-2022 was the head of the projects supported by RFBR: 16-34-60187, "Fighting drug resistance to HIV-1 reverse transcriptase inhibitors" and RSF: 17-75-10187, "Analysis of HIV resistance mechanisms to HIV reverse transcriptase and protease inhibitors using bio- and chemoinformatics approaches"; 19-75-10097, "Analysis of the interactions between HIV and human organism considering prescribed HIV/AIDS therapy".
The laboratory research studies are conducted in collaboration with the Laboratory of Structure-Function Drug Design, headed by Corresponding Member of the Russian Academy of Sciences, Prof. V.V. Poroikov. The laboratory collaborates with the M.P. Chumakov Federal Scientific Center for Research and Development of Immunobiological Drugs of the Russian Academy of Sciences and FBIS Central Research Institute of Epidemiology of Rospotrebnadzor.
The staff of the laboratory has established stable cooperation with Federal State Budgetary Educational Institution of Further Professional Education "Russian Medical Academy of Continuous Professional Education" of the Ministry of Healthcare of the Russian Federation. In particular, computer models developed by researchers of the laboratory were used in studies of clinical pharmacologists and were described in the following publications: [Ivashchenko D.V. et al., 2018, DOI: 10.1515/dmpt-2017-003630], [Otdelenov V.A. et al., 2020, DOI: 10.37489/2588-0519-2020-S4-103-105], [Kiselev Y.Y. et al., 2020, DOI: 10.37489/2588-0519-2020-S4-75-80].
The laboratory's researchers carry out collaborative studies with researchers from the Federal University of Alfenas, Brazil.
Stolbov L.A., Rudik A.V., Stolbova E.A., Pokrovskaya A.V., Shemshura A.B., Kireev D.E., Lagunin A.A., Filimonov D.A., Poroikov V.V., Tarasova O.A. (2026) A computational approach for classification of HIV drug resistance based on the Self-Consistent Extreme Classifier, Computer Methods and Programs in Biomedicine, 278, 109268. DOI:10.1016/j.cmpb.2026.109268
Tarasova O., de Azevedo Junior W.F. (2025) Cyclin-Dependent Kinases in Antiviral Drug Discovery, Current Medicinal Chemistry, 32(34), 7458-7474. DOI:10.2174/0109298673334631241208131015
Stolbova E.A., Pokrovskaya A.V., Shemshura A.B., Kireev D.E., Lagunin A.A., Sobolev B.N., Ivanov S.M., Tarasova O.A. (2025) Early Transcriptomic Signatures of Immune Response Modulation Following Antiretroviral Therapy in HIV-Infected Patients, International Journal of Molecular Sciences, 26(21), 10678. DOI:10.3390/ijms262110678
Тарасова О.A., Бизюкова Н.Ю., Столбова Е.А., Столбов Л.А., Такташов Р.Р., Карасев Д.А., Ионов Н.С., Иванов С.М., Дмитриев А.В., Рудик А.В., Дружиловский Д.С., Соболев Б.Н., Филимонов Д.А., Поройков В.В. (2024) Извлечение информации о взаимодействии вирусов с организмом человека и о противовирусных соединениях на основе интеллектуального анализа больших коллекций текстов, Биомедицинская химия, 70(6), 469-474. DOI:10.18097/PBMC20247006469
Ivanov S.M., Lagunin A.A., Tarasova O.A. (2024) Analysis of transcription profiles for the identification of master regulators as the key players in glioblastoma, Computational and Structural Biotechnology Journal, 23, 3559-3574. DOI:10.1016/j.csbj.2024.09.022
Stolbova E.A., Stolbov L.A., Filimonov D.A., Poroikov V.V., Tarasova O.A. (2024) Quantitative Prediction of Human Immunodeficiency Virus Drug Resistance, Viruses, 16(7), 1132. DOI:10.3390/v16071132
Biziukova N.Yu., Ivanov S.M., Tarasova O.A. (2024) Identification of Proteins and Genes Associated with Hedgehog Signaling Pathway Involved in Neoplasm Formation Using Text-Mining Approach, Big Data Mining and Analytics, 7(1), 107-130. DOI:10.26599/BDMA.2023.9020007
Paremskaia A.I., Rudik A.V., Filimonov D.A., Lagunin A.A., Poroikov V.V., Tarasova O.A. (2023) Web Service for HIV Drug Resistance Prediction Based on Analysis of Amino Acid Substitutions in Main Drug Targets, Viruses, 15(11), 2245. DOI:10.3390/v15112245
Rhee S.-Y., Boehm M., Tarasova O., Di Teodoro G., Abecasis A.B., Sönnerborg A., Bailey A.J., Kireev D., Zazzi M., the EuResist Network Study Group, Shafer R.W. (2022) Spectrum of Atazanavir-Selected Protease Inhibitor-Resistance Mutations, Pathogens, 11(5), 546. DOI:10.3390/pathogens11050546
Biziukova N., Tarasova O., Ivanov S., Poroikov V. (2020) Automated Extraction of Information From Texts of Scientific Publications: Insights Into HIV Treatment Strategies, Frontiers in Genetics, 11, 618862. DOI:10.3389/fgene.2020.618862