Bioinformatician

• Feb 2023 - Present

Freelancer (Freiberufler) in Bioinformatics and Data Science

• Feb 2023 - Present

*B2B with Ardigen (CRO Department https://ardigen.com/digital-cro/) *B2B with Ardigen (CRO Department https://ardigen.com/digital-cro/)

Bioinformatics Scientist

• May 2021 - Nov 2021

PhD Student in Bioinformatics

• Oct 2015 - Apr 2021

Ph.D. Student in the group of Dr. Altuna Akalin in the Bioinformatics & Omics Data Science Platform at the Max Delbrück Center (the Berlin Institute for Medical Systems Biology). My Ph.D. work provided novel insights into gene regulation and transcription factor binding due to DNA methylation dynamics in cancerous and non-cancerous cells.• Performed exploratory analysis of high-risk paediatric cancer neuroblastoma by using clinical dataderived from solid tumor samples and cell-free DNA and work collaboratively with medical doctors from the Charite hospital. Identified DNA methylation biomarkers and gene regulation abnormalities for early diagnosis and improvement of therapy choice. Applied machine learning methods such as multivariate logistic regression, elastic net / ridge regression, random forests, XGBoost. Analysed Bisulfite-seq, RNA-seq, and ChIP-seq patient-derived data.• Published a peer-reviewed publication in which I explored phenomenon of inconsistent ChIP-seq results and its common factor of poor antibody performance, and computationally and statistically segments of the genome with unusually high number of transcription factor binding sites derived from false positive ChIP-seq peaks with antibodies binding to RNA-DNA secondary structures called R-loops.• Demonstrated knowledge of Python and a workflow management system by building a Snakemake pipeline for Bisulfite-seq analysis and data visualisation called PigX Bisulfite-seq as a part of PiGX: Pipelines in Genomics.• Demonstrated knowledge of R by maintaining Bioconductor R package genomation (github.com/BIMSBbioinfo/genomation) for summary, annotation and visualization of genomic data, creating motifActivity Rpackage for computational reconstructions of transcription factor networks from sequencing data(github.com/katwre/motifActivity), and computational analysis provided as collection of R scriptsincluded in my publications. Show less

Visiting Predoctoral Researcher

• Mar 2015 - Aug 2015

The scholarship was awarded by the Institute of Computer Science Polish Academy of Sciences and co-financed out of EU funds. • I worked on development and maintenance of an Bioconductor R package genomation (git- hub.com/BIMSBbioinfo/genomation) created for summary, annotation and visualiza- tion of genomic data and project on genomic regions with unusually high number of transcription factor binding sites. Project under supervision of Dr. Altuna Akalin. • Collaborated with the IPI PAN Institute, conducted monthly progress presentations and reports Show less

Research Intern

• Aug 2014 - Sep 2014

Pipeline for the hemagglutinin influenza A-virus functional dynamics analysis in Python and using the ProDy package. Pipeline for the hemagglutinin influenza A-virus functional dynamics analysis in Python and using the ProDy package.

Research Intern

• Oct 2012 - Dec 2012

Django based metaserver for bioinformatic of RNA Django based metaserver for bioinformatic of RNA

Research Intern

• Jun 2011 - Oct 2011

MSA-VIS - Django based server for visualization of protein multiple sequence alignment MSA-VIS - Django based server for visualization of protein multiple sequence alignment