I worked in different institutions around Europe studying animal biochemistry, human genetics, bacteriology, plant biology and bioinformatics.
I am independent in experiment design and vast of molecular biology techniques, but especially I like RNA biology.
My strong sides are analytic mindset together with dedication to work. I am inspired by great ideas and like people, thinking out of the box
Here is the summary of qualifications I have:
Model organisms and cell lines: Physcomitrium patens, Arabidopsis thaliana, E. coli, Ensifer meliloti, Medicago sativa, Trypanosoma brucei, Vibrio sp.; HeLa cells.
Generation of mutant and expression constructs in most of these organisms from the design of primers to verified lines. Maintenance, sterile work with plant, human cell culture, as well as bacteria culture; skills at BSL3-4 levels (certified in Russia, not verified in Europe).
Molecular biology:
DNA: all kinds of work with DNA, from extraction and genotyping to cloning and DNA methylation profiling (bisulfite sequencing), CRISPR-Cas9.
RNA: RNA-seq: from tissue RNA extraction to differential expressed genes, including low-input, picograms amounts of RNA protocols (SmartSeq2 conversion); RACE, and RT-PCR;
Protein: from the design of the construct to purification from E.coli by FPLC or gravity flow
Microscopy: BF, epifluorescence, confocal, airyscan; image analysis (counting, area of interest comparison by masking and other using FIJI; FIJI automatization)
In silico:
- bioinformatics: Multiple alignments (Clustal, Blast) and phylogenetic trees construction with JalView, MEGA, UGENE. Analysis of RNA-Seq data from raw reads to DGE values; analysis of bisulfite sequencing data from raw reads to DMRs. Genome browsers: SeqMonk, IGV, IGB
- genetic engineering: restriction/digestion molecular cloning, Gateway/AQUA cloning; workflow from competent cell preparation to the ready construct. CRISPR-Cas9 design and application or mutagenesis. Fusion (over)expression constructs; very good knowledge of SnapGene and Benching in-built molecular genetics tools.
- programming for biology: Unix independent user, bash/shell scripting. Conda environments and SnakeMake. Perl, and R (RStudio) basic programming. Confidence in Python and BioPython. Working with IDE (PyCharm), Jupiter notebooks. Active user of GitHub and Galaxy; NCBI, EBI, and Expasy tools; NCBI e-utilities, biomart
- statistics and graphics: RStudio (deseq2, edgeR, different plotting tools), Python (Pandas, Matplotlib, seaborn); image analysis with FIJI (ImageJ), automatization of processes