Research group Bioinformatics
The Bioinformatics research group brings together biology and computer science to address key challenges in health, the environment, and microbiomes through smart data analysis, multidisciplinary collaboration with domain experts, and the development of user-friendly applications.
The Bioinformatics research group plays a vital role in the applied research conducted at the Leiden Centre for Applied Bioscience (LCAB). Our latest insights in bioinformatics contribute to professional practice, society at large, education, and knowledge development across the various research domains within the LCAB.
Working method
In the professional field, bioinformatics is highly valued for the cross-disciplinary advantage it brings to collaborative research teams. Navigating the journey from raw biological sample to innovative biological insight is virtually unthinkable today without bioinformatics.
For more than a decade, the Bioinformatics research group has positioned nanopore sequencing as a core enabling technology. Data management and processing are central to every stage of our workflow. Developing applications, databases, and analysis pipelines has become our core business. To empower non-bioinformaticians with computational workflows, we leverage Galaxy, while Nextflow systems are utilised for robust, reproducible, high-throughput applications.
In addition, we advise the Bioinformatics degree programme on curriculum innovation, develop instructional materials, and deliver guest lectures across various study tracks. We provide students with hands-on research opportunities through minors, short internships, and graduation projects. We also actively contribute to the professional development of both our lecturing staff and industry professionals.
Impact
Our research simplifies data processing and facilitates data interpretation in the complex realms of biology and chemistry. We support LCAB research professors (lectoren) and train emerging talent during and beyond their degree programmes.
Furthermore, we focus on innovative applications of nanopore sequencing and modern technologies like knowledge bases to make biological data more accessible. A prime example is our application that detects microbiological contamination in the food processing industry while simultaneously tracing it back to its point of origin.
Education
We keep our educational programmes closely aligned with the latest industry standards by feeding real-world practical insights back into the curriculum - incorporating tools such as Git, Docker, cluster computing, and modern data science techniques.
The research group trains students and early-career researchers in cutting-edge bioinformatics: from foundational programming skills to engineering end-to-end analytical pipelines. Through practice-oriented projects, they gain experience working with real-world datasets and actual research questions, preparing them for careers in research, healthcare, or the biotechnology industry.
- Curriculum support: We assist degree programmes with module and minor design, nanopore sequencing applications, and the coordination of research internships and capstone projects.
- Continuing education: We deliver short professional courses for the Centre for Bioscience and Diagnostics (Centrum Bioscience en Diagnostiek - CBD), the specialised training centre for professionals in life sciences and health.
Onze onderzoeksprojecten
We provide data analysis and visualisation support to all research groups within the LCAB. In addition, we actively participate in projects dedicated to internal methodology development.
Metatranscriptome of Kombucha
In complex microbial communities, our goal is not just identifying which species are present, but also determining what functions they perform. Kombucha is a classic example: in this project, we characterise the microbial community and investigate the precise biochemical roles and interactions within the culture.
Advanced Precision in Food Safety (Completed)
How can microbial contamination sources be precisely identified? Building on prior food safety research, this project expanded beyond Listeria monocytogenes to target Salmonella and toxin-producing Escherichia coli. We also analysed the genomic characteristics of Listeria monocytogenes isolates to determine whether specific strains are virulent or particularly resilient in food processing environments.
Omics in de Polder (Completed)
The peat meadow landscape (veenweidegebied) in the Netherlands is ecologically unique yet under severe environmental pressure. It serves multiple competing functions: agriculture, housing, nature conservation, recreation, infrastructure, and water storage. Amid climate change, biodiversity loss, land subsidence, and housing shortages, this project evaluated spatial and biological solutions to promote sustainable agriculture and enhance local biodiversity.
Fermentobiomics (Completed)
Fermented foods such as sourdough bread, kefir, and kombucha have surged in popularity, prompting industrial producers to scale up manufacturing. To support food manufacturers, this project examined the underlying biological mechanisms of fermentation. By characterising the microbial dynamics (the fermentbiome) across the fermentation lifecycle using multi-omics techniques, we mapped this complex biological process in detail.
Hidden Biodiversity
Urban environments harbour a surprising amount of undocumented biodiversity. Led by Naturalis Biodiversity Center, this collaborative initiative brings together municipalities, businesses, universities, and universities of applied sciences to uncover and map hidden urban biodiversity.
Interne methodenontwikkeling
Implementation of Adaptive Sequencing
Nanopore sequencing is a cornerstone technology for our group, and keeping state-of-the-art sequencing methods in-house is central to our mission. Adaptive sequencing allows for the real-time targeted enrichment or depletion of specific DNA/RNA molecules directly on the sequencer. Over the past year, we have implemented:
- Real-time bacterial identification.
- Barcode-based read-balancing across multiplexed samples.
- Identification of Bacillus species based on toxin-encoding gene profiles.
- Depletion of host DNA in metagenomic samples during sequencing runs (currently under development)
Deployment of Nextflow Tower for High-Throughput Analyses
Automating data workflows is a continuous priority across our diverse project portfolio. The breadth of our research requires a robust, centralised infrastructure capable of launching workflows across multiple compute environments. Nextflow (and Nextflow Tower) meets these requirements effectively and remains under active development within our group.
Ons netwerk
Our Network & Collaborations
The Bioinformatics research group works in close collaboration with regional businesses, universities, and research institutes:
- LCAB Research Groups: Our primary internal collaboration partners include the Food, Health & Innovation and Environmental Metagenomics research groups.
- Microbial Genomics Consortium: We collaborate closely with the consortium partners of the Advanced Precision Food Safety project led by the Microbial Genomics research group.
Contact & Information
The Bioinformatics research group is part of the Leiden Centre for Applied Bioscience (LCAB) at University of Applied Sciences Leiden (Hogeschool Leiden).
For collaboration inquiries, research opportunities, or further information, please contact email: [email protected]