Biography
I am a senior bioinformatics research scientist at Department of Pathology, Institute of Clinical Medicine, University of Oslo, Norway and working in the Jahnsen lab.
⚡ I have been developing open-source bioinformatics tools downloaded by thousands including MirMachine and cellsnake.
🔭 My research interests include biostatistics, bioinformatics, molecular epidemiology, spatial transcriptomics, single-cell and bulk RNA sequencing, early detection of cancer using ML and AI, RNA biology of cancer and RNA-RNA interactions.
🔭 I also have bioinformatics pipelines written in Snakemake (also in Python and R) like a small RNA sequencing pipeline, sncRNA-workflow, or a WGS pipeline for HPV variant detection (TaME-seq)
🌱 I completed my doctoral studies in the fields of Biotechnology and Bioinformatics at the University of Canterbury in New Zealand. My research concentrated on the non-coding RNAs in prokaryotic organisms. The primary emphasis of my dissertation was on the interactions between non-coding RNAs and messenger RNAs within the genomes of bacteria and archaea.
The tools that I developed and published:
| Tool | Download | Purpose |
|---|---|---|
| MirMachine |  | microRNA homology search tool using machine learning |
| Cellsnake |  | single-cell analysis tool for everyone |
Research Interests
- Modelling and early prediction models in the context of personalized medicine
- Molecular oncology and cancer
- RNA biology, especially non-coding RNAs such as microRNAs, tRNA-derived molecules
- RNA-RNA interactions
- Biostatistics and molecular epidemiology
- NGS (DNA and RNA sequencing), transcriptomics from bulk RNA sequencing to spatial transcriptomics
- Reproducible bioinformatics pipelines, mostly using Snakemake, shell scripts, Python and R programming
Skills
- R, I am quite capable in tidyverse syntax (ggplot, caret, mlr3, Rmarkdown, shiny apps, functional programming, parallelization)
- Machine learning and data analysis in R
- Python (especially in bioinformatics context)
- Snakemake (I develop pipelines and also teach Snakemake)
- Biostatistics (basic modeling, survival models, and some newer machine learning algorithms)
- Linux (shell scripting and high-performance computing systems)
- Data Science and Machine learning (for predictive models, especially in R and Python, h2o, caret, Keras)