RNAldo: Exploring a new long-read RNA Sequencing Analysis Pipeline

Fermentation-based biomanufacturing underpins the sustainable production of high-value fine chemicals such as colorants, hormones, enzymes, alternative proteins, and mycelium-based materials. However, molecular monitoring tools which reveal what happens inside microbial cells during fermentation remain underused in applied research and industry, especially within universities of applied sciences (hogescholen) due to the complexity and high cost of the technology.
This fellowship aims to develop an accessible and affordable RNA level workflow for fermentation process monitoring together with knowledge and industrial partners. Meanwhile, the research topic will be implemented in education. The focus of the project is on establishing a data driven, user-friendly, and scalable workflow that allows both researchers and industrial partners to understand microbial behavior and control production efficiency on molecular level.
The fellow, Bazante Sanders (Avans Hogeschool, MNEXT), will focus on building RNAldo - a one-stop analytical platform that integrates bioinformatics tools for RNA-sequencing data analysis, visualization, and interpretation. The project will also explore advanced single-cell RNA data analysis as an emerging option for understanding population-level heterogeneity in industrial fermentation.
By integrating this technology into the Bioinformatics learning module at the Avans School of Life Sciences and the Smart Fermentation research line at MNEXT, the fellowship will not only strengthen HBO education and equip candidates with cutting-edge technical skills but also give regional SMEs access to advanced molecular analytics. In doing so, it will support innovation across the region and contribute to a more robust local job market by preparing students for emerging roles in this field.
Main impact areas:
• KIA 6 – Key Enabling Technologies: digital biomanufacturing and molecular analytics.
• KIA 2 – Circular Economy: optimizing sustainable microbial processes for material and chemical reuse.