Allele-Specific Expression and Single-Cell Analysis at BioBam Bioinformatics
From February 2 to March 30, 2026, Nadja Franziska Nolte, LongTREC Doctoral Candidate at the National Institute of Biology (NIB), had the opportunity to carry out a research secondment at BioBam Bioinformatics, supervised by Stefan Götz. This secondment offered valuable growth, both in scientific expertise and personal development.
My goal? The initial goal was functional annotation of my potato data. As this was already complete before the secondment began, we set new goals: testing my allele-specific expression pipeline on a customer’s sweet potato dataset, and testing the OmicsBox single-cell pipeline on potato single-cell data.
Nadja reflects on her experience:
What I Learned 🎓
I ran the full LongPolyASE pipeline on sweet potato direct ONT data. The sequencing depth was too low for detailed allele-specific expression analysis, so I wrote documentation and scripts to repeat the analysis when new data is available.
Takeaways 🌱
Testing the OmicsBox single-cell pipeline on potato data, I identified improvements to its settings.
Impact 🌟
I also wrote a blog post on allele-specific expression with long-read RNA-seq and phased reference genomes.
Overall, this secondment applied my pipeline to real customer data and contributed to BioBam’s single-cell tools.
