Background:

While studying at the Department of Microbiology, Faculty of Biology, I was engaged in compiling a collection of anaerobic cellulolytic bacteria, picked up the optimal conditions for anaerobic fermentation of paper waste. Developed microbial fuel cells powered by anaerobic hydrolyzed paper. Participated in a project to study the microbial biodiversity of the Antarctic Lake Vostok. During my graduate studies, I developed combinations of antimicrobial agents to combat multidrug-resistant pathogenic bacteria. Developed antimicrobial peptides active against pathogenic bacteria and fungi. Developed antimicrobial peptides that inhibit the translation of bacteria. Participated in the development of a screening system for the search for new translation inhibitors. Developed a pipeline for the search for neoantigens in the human immunopeptidome. Worked on the creation of a system for processing and storing biological data. Developed algorithms for prioritizing molecular targets of clinically important human diseases. Developed an algorithm for generating explanatory schemes for the mechanism of the possible pathogenesis of human diseases.

Skills:

Bioinformatics/Information technology 

• Linux
• Bash scripting
• Python
• SQL
• Docker
• Postgres
• Neo4J
• MongoDB
• Jupyter-notebook
• ETL scripting 
• Data cleaning/normalization
• Assembly proteomics databases
• Working with biology databases(NCBI, Pubchem, Chembl, StringDB, Reactome...)

    Molecular biology/Microbiology

• Basic work with: E.Coli, S. aureus, P. aeruginosa, Saccharomyces cerevisiae, Aspergillus niger
• A microbial culture medium preparation
• Buffer preparation
• Antimicrobial susceptibility testing
• Fluorescent microscopy
• DNA/RNA extraction
• PCR
• Design of primers
• cDNA cloning
• Gel electrophoresis (DNA,Protein)
• Restriction enzyme analysis
• DNA ligation
• Expression and purification of recombinant protein in bacterial system
• Purification by affinity tag chromatography
• Cell-free protein synthesis
• HPLC
• Sample preparation for LC-MS
• Immunoprecipitation
• Western-blot
• ELISA

Scientific interests:

• Host-Pathogen Interactions
• Bacterial Cell–Cell Communication
• Gene regulatory network
• Automated reconstruction of human signaling networks
• Information retrieval from biomedical texts
• Construction of biology knowledge graphs

English - Upper intermediate

Internships

5th Summer School in Molecular Biophysics and Systems Biology, Nove Hrady, South Bohemia, Czech Republic, July -August 2017

Conferences

XXX Winter Youth Science School in Shemyakin – Ovchinnikov Institute of Bioorganic Chemistry RAS, oral presentation, Feb 2018, Moscow, Russia

Publications

1. Naumov, V., Putin, E., Pushkov, S., Kozlova, E., Romantsov, K., Kalashnikov, A., ... & Zhavoronkov, A. (2021). COVIDomic: A multi-modal cloud-based platform for identification of risk factors associated with COVID-19 severity. PLoS computational biology, 17(7), e1009183.
2. Bolosov, I. A., Kalashnikov, A. A., Panteleev, P. V., Ovchinnikova, T. V. .Analysis of Synergistic Effects of Antimicrobial peptide Arenicin-1 and Conventional Antibiotics. Bulletin of Experimental Biology and Medicine. (2016) 162(12).
3. Samkov, A. A., Volchenko, N. N., Khudokormov, A. A., Kalashnikov, A. A., & Veselovskaya, M. V. Anaerobic biodegradation of organic compounds in microbial fuel cells. Polythematic Online Scientific Journal of Kuban State Agrarian University.(2014) 101(07) [Russian]
4.  Samkov, A. A., Volchenko, N. N., Veselovskaya, M. V., Kalashnikov, A. A, & Khudokormov, A. Benthic microbial fuel cell in freshwater bottom sediments. Applied Technologies & Innovations. (2013) 9(4)