About me
Academic Degrees
Associate Professor 𓀍 in Bioinformatics, Uppsala University, Uppsala, Sweden, 2019.
Doctor of Philosophy 𓀊 in Bioinformatics, Uppsala University, Uppsala, Sweden, 2010. Linnaeus Centre for Bioinformatics, advisor prof. Jan Komorowski. Thesis: From Physicochemical Features to Interdependency Networks: A Monte Carlo Approach to Modeling HIV-1 Resistome and Post-translational Modifications.
MSc 𓀤, Uppsala University, Uppsala, Sweden, 2005. Major: molecular biology, minor: chemistry.
BSc 𓀧, Warsaw University, Warsaw, Poland, 2003. Area: molecular biology.
Experience
Bioinformatics Data Scientist, Science for Life Laboratory, National Bioinformatics Structure, Sweden. Uppsala, Sweden, 2017 – now.
Researcher, Kerstin Lindblad-Toh’s Lab, Department of Medical Biochemistry and Microbiology, Uppsala University, & Science for Life Laboratory, Uppsala, Sweden, 2014 – 2017.
Assistant researcher, Örjan Carlborg’s Lab, Computational Genetics Group, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Sweden, 2010 – 2014.
Postdoctoral researcher, Örjan Carlborg’s Lab, Computational Genetics Group, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Sweden, 2010 – 2014.
PhD student, The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden, 2006 – 2009.
Web consultant and database engineer, Global Diversity Foundation, 2006 – 2010.
Programming Languages
| Language | Skill | Comment | |
|---|---|---|---|
| bash | 95% | daily routine advanced use | |
| R | 98% | daily advanced usage, teaching advanced R | |
| Python | 80% | frequent advanced use, esp. for deep learning | |
| µ | uPython | 90% | frequent advanced usage for microcontroller programming |
| C | 75% | frequent use for microcontroller programming | |
| Java | 75% | frequent advanced use in the past | |
| LISP | 50% | used for fun and for teaching purposes | |
| PERL | 40% | used some time ago | |
| Fortran | 30% | used some time ago | |
| Julia | 5% | want to learn | |
| JS | 45% | using quite frequently | |
| HTML5 | 80% | using frequently | |
| markdown | 87% | daily usage of RMarkdown & Quarto | |
| SQL | 60% | frequent usage from time to time |
Tools
- Docker,
- Singularity,
- Snakemake,
- Nextflow,
- OpenSCAD,
- Keras,
- Jupyter, RStudio, Wordpress etc.
Other skills
- system administration,
- 3D printing & parametric design,
- soldering,
- µC programming (Arduino, RPi Pico family),
- electronic circuit analysis & design,
- boating/navigation (Coastal Yahtsmaster Diploma, Marine VHF license),
- radio digital modes,
- home automation,
- woodworking,
- wet biological lab (Radiation Safety License)