Profile
Computational biologist with a PhD in bioinformatics and microbiology. I build pipelines and open-source tools in Nextflow, Python and R, and use them on large sequencing datasets.
My work covers metagenomics, transcriptomics, phylogenomics, functional annotation and machine learning. During my PhD I cleaned and analysed 19,720 metagenome-assembled genomes with a pipeline I wrote and released, and ran a year-long cultivation study to isolate the bacteria behind them.
Available from 1 October 2026.
Work Experience
Postdoctoral researcher
Jan 2026 - Nov 2026Medema group, Bioinformatics group, Wageningen University & Research
- Mined marine sponge metagenomes for biosynthetic gene clusters, and selected candidates for downstream heterologous expression
PhD Candidate
Jan 2022 - Dec 2025Medema group & Detmer Sipkema lab, Bioinformatics group & Molecular Ecology group, Wageningen University & Research
Project: Treasures of the deep — biosynthetic profiling and cultivation of marine host-associated Acidobacteriota
- Planned and led a year-long, uninterrupted isolation study of sponge-associated bacteria under unconventional cultivation conditions, uncovering new physiological properties in the isolates
- Built a Nextflow pipeline that takes raw MAGs through quality filtering, chimerism removal, dereplication and taxonomic classification — used it to reduce 19,720 public Acidobacteriota genomes to a clean, species-level set.
- Mined biosynthetic gene clusters across that set with antiSMASH and BiG-SCAPE, and wrote the tooling to explore the results (an iTOL annotation generator and a BiG-SCAPE domain-co-occurrence app)
- Analysed 488 marine genomes across 16 families to separate host adaptation from shared ancestry, combining phylogenomics, Pfam-based feature matrices and random forest models
- Used functional predictions from the metagenomes to design the isolation media, closing the loop between the computational and the wet-lab work
- Supervised 2 MSc and 1 BSc student across both computational and molecular work
- Presented at 11 multidisciplinary conferences across microbiology, bioinformatics and natural products
Technical Support Specialist
May 2021 - Oct 2021Information System Development
- Reproduced and diagnosed reported bugs against testing servers in a regulated, HIPAA-compliant environment
Laboratory Technician
May 2020 - Dec 2020Ivan Franko National University of Lviv
- Sequenced, assembled and annotated the complete genome of Streptomyces cyanogenus S136, producer of the anticancer angucycline landomycin A (published in 3 Biotech)
- Wrote two open-source tools during this period — rRNADif and BGCViz — and carried out the phylogenetics and BGC mining behind them
Selected Software
Open source, documented, and on GitHub. Full list on the Tools page.
ashelper
2026Turns antiSMASH and BiG-SCAPE output into iTOL annotation files.
MAG Cleaning Pipeline
2026Nextflow pipeline that takes a directory of metagenome-assembled genomes and returns a dereplicated, quality-filtered, taxonomically classified set
BGCViz
2020pfam_tools
2026Scans proteomes against Pfam-A, builds a QC-filtered presence/absence matrix, and annotates it with GO terms
Contributions to other projects
metaWRAP — A widely used metagenome binning and analysis pipeline. I contributed a processing of nanopore reads RepositoryMy commits
Arrower — Draws gene cluster arrow diagrams from a GenBank file as SVG. I revived an abandoned Python 2 script: ported it to Python 3, gave it a real CLI, and added category-based arrow colouring with a legend. GitHubMy commits
Technical Skills
Languages
Python, R, Bash, SQL
Workflows & reproducibility
Nextflow, Conda, Git, working on remote Linux servers, R packaging, Shiny
Bioinformatics
Large-scale metagenomics and metatranscriptomics, BGC mining (antiSMASH, BiG-SCAPE, MIBiG), phylogenomics, functional annotation (Pfam, GO, HMMER/pyhmmer)
Statistics & ML
Statistical analysis in R and Python, random forests, clustering, enrichment testing, data cleaning and exploration
Laboratory
Cultivation of slow-growing and marine bacteria, E. coli and Streptomyces work, heterologous expression, (q)PCR
Education
M.Sc. in Genetics and Biotechnology
Sep 2019 - Dec 2020Ivan Franko National University of Lviv
Diploma cum laude. Thesis: Genome of S.cyanogenus S136: secondary metabolism potential
- Performed biosynthetic gene cluster mining in S.cyanogenus S136 genome
- Developed software to support the analysis
B.Sc. in Biology
2015 - 2019Ivan Franko National University of Lviv
Thesis: Genetical control of morphogenesis in S.cyanogenus S136
- Performed heterologous expression of selected gene clusters
- Analysed phylogeny of rodlins and chaplins in Streptomycetaceae
Teaching Experience
Practical Computing for Biologists - Teaching Assistant
Fall 2024Wageningen University & Research
- Assisted with providing practical advice for students during the assignments
Research methods in microbiology - Teaching Assistant
Winter 2024Wageningen University & Research
- Developed course materials for computational part of the course
- Assisted with teaching and practicals for the part of the course
- Graded assignments and provided detailed feedback
Practical Computing for Biologists - Teaching Assistant
Fall 2023Wageningen University & Research
- Assisted with providing practical advice for students during the assignments
Awards & Honors
Invited speaker
2025Summer School for Natural Products research 2025
Grant
202019th European Conference on Computational Biology participation grant, Barcelona, Spain
Top 3 projects
2020Data Engineering and Security winter school (DES 2020), Lviv, Ukraine
1st place
20194th Advanced in silico Drug design workshop/hackaton 2019, Olomouc, Czech Republic
Languages
English
Advanced (C1)
Ukrainian
Native
Dutch
Beginner (A1)