I studied at Physics Faculty, at the University of Warsaw, Poland, where I also did my Ph.D. in theoretical biophysics under the supervision of Assoc. Prof. Joanna Trylska. During my Ph.D. studies, I was investigating the resistance mechanisms of bacteria against aminoglycoside antibiotics. I used tools of theoretical biophysics, such as molecular dynamics (MD) simulations, Poisson-Boltzmann electrostatic model, molecular mechanics (MM) generalized Born (GB) surface area (SA) free energy estimation and many visualization techniques. I developed an algorithm for analysis of internal motions of biomolecules based on large conformational datasets e.g., from MD simulations. The algorithm is implemented in Java standalone program, Geometrically Stable Substructures (GeoStaS) - check it out on bitbucket!
Next, I spent two years at the Heidelberg Institute for Theoretical Studies (the MCM group of Prof. Rebecca Wade), where I was studying interactions of biomolecules within a crowded and confined environment, which mimics the cellular interior. I was using Brownian Dynamics (BD) simulations and was developing a model for biomolecules interacting with solid surfaces. My programming skills were useful in the development of the new version of SDA (Simulation of Diffusional Association). Moreover, I was studying association and dissociation kinetics of drug-protein complexes, also using BD simulations.
As a post-doc at the University of Bergen, I was analyzing genomic data with the use of statistical methods, and looking at possible risks for certain phenotypes associated with specific allele variations. I am involved in the development of the Haplin software, intended for this kind of analysis. The project was a joint collaboration between Prof. Rolv Terje Lie at IGS and Prof. Inge Jonassen at CBU, which aimed at making the software more efficient and available to a larger scientific community, as well as including bioinformatics data into the analysis. After that, I was a researcher involved in quality control analyses of a unique collection of DNA methylation data for START project (Study of Assisted Reproductive Technology), at Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo and Department of Global Public Health and Primary Care, University of Bergen, Bergen.
Currently, I am a bioinformatics expert (senior engineer) at BIOS (https://www.uib.no/en/rg/biostatistics), where I use my expertise in data science, structural bioinformatics, programming, and data visualization to explore big data, efficiently run complex analyses, and visualize results. Apart from that, I am a co-founder of R-Ladies Bergen (https://www.meetup.com/rladies-bergen/), a chapter of R-Ladies Global, which is an organization to promote gender diversity in the R community.
- 2020. Gene-methylation interactions: Discovering region-wise DNA methylation levels that modify SNP-associated disease risk. Clinical Epigenetics. 18 pages.
- 2020. Design efficiency in genetic association studies. Statistics in Medicine. 1292-1310.
- 2019. Haplin power analysis: a software module for power and sample size calculations in genetic association analyses of family triads and unrelated controls. BMC Bioinformatics. 11 pages.
- 2019. From genotype to phenotype: Through chromatin. Genes. 16 pages.
- 2019. A genome-wide scan of cleft lip triads identifies parent-of-origin interaction effects between ANK3 and maternal smoking, and between ARHGEF10 and alcohol consumption. F1000 Research. 28 pages.
- 2018. Analysis of parent-of-origin effects on the X chromosome in asian and european orofacial cleft triads identifies associations with DMD, FGF13, EGFL6, and additional loci at Xp22.2. Frontiers in Genetics. 17 pages.
- 2018. A genome-wide search for gene-environment effects in isolated cleft lip with or without cleft palate triads points to an interaction between maternal periconceptional vitamin use and variants in ESRRG. Frontiers in Genetics. 16 pages.
- 2017. Parent-of-origin-environment interactions in case-parent triads with or without independent controls. Annals of Human Genetics. 60-73.
- 2017. Genome-wide analysis of parent-of-origin interaction effects with environmental exposure (PoOxE): An application to European and Asian cleft palate trios. PLOS ONE. 19 pages.
- 2017. A new approach to chromosome-wide analysis of X-linked markers identifies new associations in Asian and European case-parent triads of orofacial clefts. PLOS ONE. 23 pages.
- 2015. When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces. Nano Letters. 7508-7513.
- 2015. SDA 7: A modular and parallel implementation of the simulation of diffusional association software. Journal of Computational Chemistry. 1631-1645.
- 2015. Haplin — a powerful tool for studying gene-environment interactions.