Investigating Muscle Precursor Diversity with scRNA-Seq: Meet the Genevia RNA-Seq Bioinformatics Grant Winner
Late 2024, we launched the second Genevia RNA-Seq Bioinformatics Grant – an opportunity for an academic research group to win fully tailored bioinformatics support for a transcriptomic project. Among the many innovative, high-quality applications spanning a wide range of research areas and data types, one stood out. On February 6th, 2025, we announced Dr. Josephine Bageritz from Heidelberg University as the winner. Her single-cell transcriptomics project aims to deepen our understanding of spatially regulated signaling in muscle stem cell regulation during development. Proud of the science we help enable and the brilliant researchers we work with, we want to highlight their stories: here, Dr. Bageritz shares more about her work and the grant-winning project.
Dr. Josephine Bageritz
Passion in stem cell biology
Dr. Josephine Bageritz’s career has been driven by her long-standing curiosity about stem cell biology. She began working with stem cells during her PhD, initially focusing on tumor stem cells, before shifting, in her postdoc, to using Drosophila as the model system for studying neural stem cells and undifferentiated epithelial cells. In 2021, Dr. Bageritz moved to the Centre for Organismal Studies (COS) at Heidelberg University, to establish her independent research group, focusing on the heterogeneity of muscle stem cell niches.
– I’m leading a small team investigating how adult muscle cells are regulated during their development in terms of their number and heterogeneity, and how this impacts adult organismal life, she explains.
– In other words, we’re connecting development with adult muscle function and regenerative capacity as well as muscle mass and strength. I’m using Drosophila as the model system, and through collaborations, we’re applying our knowledge to higher organisms.
At the Bageritz lab, single-cell and spatial transcriptomic technologies are used to characterize cell heterogeneity as well as heterogeneous cellular responses to RNAi and CRISPR-based perturbations. This transcriptomics-based branch – where Genevia Technologies will participate – is complemented by sophisticated imaging and AI-based approaches to analyze cellular phenotypes.
Dr. Bageritz’s experience with omics technologies traces back to her early career, beginning with microarrays and bulk RNA sequencing. During her postdoc, as single-cell technologies started to evolve, she worked in Michael Boutros’ lab in Heidelberg, using Drop-seq data from isolated cells to reconstruct spatial gene expression patterns. As these technologies became more prominent, she realized the importance of strengthening her computational analysis skills, and dived into it by online courses and discussions with colleagues from computational backgrounds.
– In fact, we still use those techniques from my postdoctoral work because they have certain advantages, but now that there are more advanced spatial transcriptomic methods available, we apply those as well to directly profile cells in their niche environment.
The grant-winning project
The Bageritz lab consists of about six people, most of whom specialize in the imaging side of the research. As a group leader, Dr. Bageritz has limited time for data analysis, and while her team is eager to learn, mastering bioinformatics takes time. Additionally, she points out that finding a good bioinformatician is always challenging, especially for a young group. This is why she’s been considering outsourcing bioinformatics for a while:
– I’m currently teaching a single-cell course for the students for the fourth time, and people in my lab are learning as well, but it takes time and requires a lot of my involvement. For a while, I’ve been thinking that this must be solved in one way or another, she reflects.
Someone on campus had mentioned Genevia Technologies to her some time ago, but she admits having been hesitant about how such a service could work for projects requiring custom analyses and close interaction; she wondered whether outsourcing bioinformatics could be a true alternative or if she should seek for an academic collaborator instead. The Genevia Bionformatics Grant 2025 came at the perfect time.
– I can’t remember if I saw it on social media or received an email about it, but applying was an easy decision. I thought that this is a nice test scenario to explore the option, she says.
The grant-winning project is funded by the German Research Foundation (DFG, Deutsche Forschungsgemeinschaft) and investigates the role of Wnt signaling for the numbers of muscle precursors during development.
– Why are they so different and how do signaling pathways integrate to control their numbers? We have some indications that Wnt signaling and some other pathways play a role in this, but we don’t fully understand how this is transmitted at the cellular level and in terms of output, Dr. Bageritz explains.
To find answers, her team perturbs these pathways in individual cell populations and observes how specific populations respond – or fail to respond.
– This project belongs to a PhD student who is highly skilled in terms of AI and imaging-based approaches. She has developed random forest classifiers to study the heterogeneity in imaging data, for instance, but when it comes to transcriptomics data, she would have to start from scratch. I think this was actually an ideal situation for the grant, she rejoices.
The project is set to start in March. Dr. Bageritz’s first impression of Genevia Technologies is very positive, and she’s looking forward to seeing how the collaboration unfolds:
– I’ve already been in contact with Genevia on various levels, which is a great start. They seem to be a very engaged, active group of bioinformaticians and computational developers. If this proves to be a great service I think it will be very useful not only for us but for many groups in Heidelberg. I’m curious and ready to dive into the project!
