Data Scientist, Bioinformatician, Tool developer and Snakemake enthusiast
LinkedIn: @chrarnold84
My activities and repositories
My main repositories from the last years are not here but at a public institutional Gitlab instance at EMBL. While some are public, others are currently not accessible publicly, however.
Selected recent highlights include:
- SUMseq processing pipeline (not public yet, currently the corresponding paper is in revision)
- diffTF (from this repository)
- GRaNIE Bioconductor/R package (from this repository)
- Teaching material for our yearly ATAC-Seq course at EMBL
- Snakemake pipelines for different types of NGS data such as bulk and single-cell RNA-seq, bulk ATAC-seq, ChIP-Seq, ... (not public yet)
One of my all-time favorite projects resulted in a high-impact publication, including a designated webserver that I programmed (as of January 2024, the SSL certificate is being renewed by the university):
During my PhD, I was more heavily involved in algorithm development and biological/chemical simulations, which resulted in the following software, for example:
- StoChDyn - Stochastic modeling of chromatin state dynamics across cell divisions and evolutionary optimization of epigenetic stability
- Targeting - An efficient software package for solving the Maximal Pairing Problem on arbitrary trees
As a developer, I am aware of the importance of identifying bugs in code. Therefore, I am also reporting bugs in various bioinformatics tools whenever I identify them. By now, I indirectly contributed to many bioinformatics-focused repositories and programs (such as samtools, Snakemake, bedtools, and various R packages).
Contact
If you're interested in my work, my future plan, how I could you with your project, I'd love to chat. I am currently working at EMBL in Heidelberg. See above for how to contact me.