Hanze University of Applied Sciences
ILST Zernikeplein 11 9747 AS Groningen
Dr. ir. J.P.H. Nap
0031 (0)50 5954794 (mon-tue-wed)
The facility has state-of-the-art bioinformatics computing infrastructure that is accredited as ‘excellent’ for research and education by the Dutch-Flemisch accreditation organization (NVAO) and first-class laboratory facilities. Research is performed by staff (at PhD level and MSc level), that is involved in research and education; students may participate when possible. Available for bioinformatics research and consultation are a dedicated team with skilled programmers (software evaluation and development) and trained biology researchers for high throughput data analysis and interpretation. We specialize on next gen DNA data analysis, data visualization and data mining. As we are close to education, explaining what we do, listening to wishes and desires of co-workers/end-users and making things work is integral part of our mode of operation. We have contributed many bioinformatics bachelors to the Dutch science community and therefore have a broad network of contacts, expertise and infrastructure.
The facility is part of the Institute for Life Science & Technology of the Hanze University of Applied Sciences is responsible for fulltime Bachelor of Applied Sciences (BAS) curricula in bio(techno)logy, medical diagnostics, chemistry, chemical technology and bioinformatics with over 800 students and 56 fte staff. The Institute has a rapidly growing research facility (ALIFE) with two professorships, one in Life Sciences including bioinformatics and a second one in Food Ingredients and Health. The institute is involved in many different research projects that focusing on the core research topics of the university, healthy ageing and energy. The institute has state-of-the-art laboratory facilities and bioinformatics computing infrastructure (the latter accredited as ‘excellent’ by the NVAO ). Research is performed by staff (predominantly at PhD-level), that is balancing research and education; students are involved when possible. Research is largely carried out in open innovation consortia in close collaboration with (small size) companies and research universities. It involves both wet lab analysis and big data bioinformatics analyses of food digestion, biogas production (metagenomics), and a variety of other projects such as SNP calling in complex genomes.
- Biomedical & health
- Agri & Food
- Industrial biotech
- Data storage/curation
- (Web-based) Visualization
- Metagenomics (whole genome and 16S) of microbial fermentation (biogas, prebiotics)
- Analytical biochemistry of microbial fermentation (biogas, prebiotics)
- SNP calling in complex (polyploid) genomes
- Accurate read mapping/alignments of output from different NGS platforms
- Microbial qPCR and qPCR primer design and evaluation
Expertise and Track Record
We bridge the gap between wet-lab research and analysis of the results of that research while focussing on application and performance. We specialize in Next-Generation Sequencing data: processing, statistical analysis and data mining, organization and storage. We combine this an excellent track record in training and explaining complex bioinformatics concepts to students, biologists and end-users. We design interfaces (both desktop applications and web-based systems) for researchers to access and organize their data and visualize the analysis. We do not necessarily aim to publish the research, are proud to make things that work and are open to both long-terms collaboration in research projects and short-term consultancy.
• Analysis of various whole genome and 16S metagenomics data sets;
• Extensive SNP calling in tetaploid potato;
• improved read mapping protocols for next generation sequencing data sets (454, Illumina);
• RNAseq analysis and integration of RNAseq with genomic data;
• Experimenting with PacBIO data and integrated cross-platform data analysis;
Development of improved alignment algorithm on cheap Graphical Processing Units;
• Analysis, visualization and storing of neurological microarray and related data;
• Primer design and validation;
• Contributed approximately 60 BAS to the Dutch bioinformatics research community over the last six years.
We collaborate with many partners from all over the Netherlands. We are partner in the Carbohydrate Competence Centre (CCC), the Healthy Ageing Network North Netherlands (HANNN), the public-private Food Circle consortium, the open innovation initiative for energy transition EnTranCE, the research program Flexigas, the Zernike Advanced Processing facility, the Energy Academy Europe (EAE), Energy Valley, Eurec and DAS. We are founding member of LOBIN. In all these networks we do application-oriented research and involve our skills, knowledge, infrastructure.
- 3 dedicated postdocs
- 2 dedicated technicians
- 1 lab manager
- 1 biostatician
- 1 IT-specialist