Internships & Projects

Projects and Internships

Bioinformatics Profile Students are expected to at least “do” a bioinformatics project (18EC) however we recommend to go for a 33EC (6 months) internship. On this page we try to list projects that are available trough our community. Of course you are always welcome to find your own group to do an internship (or project). Keep in mind to always discuss with your masters coordinator (tutor) to see if this bioinformatics internship (or project) also fits the requirements of your master.


Research projects topics

  • [Machine learning] Discovering rare DNA micro-topologies using multi-contact chromatin conformation data with single-allele resolution
  • [Bioinformatics] In-silico Unique-Molecule-Identifier (UMI) to discern single-allele conformations in 3rd generation nanopore sequencing technology
  • [Bioinformatics] Mult-way aware aligner to improve long-read (3rd generation) sequencing mapping quality
  • [Visualization] Peaking into higher-order chromatin contacts: visualizing multi-way DNA interactions in the nucleus
  • [Statistical modeling] Association test to distinguish linear proximity of sites in the genome from their 3D interactions

Several research projects in the group of Wouter de Laat


There are trillions of cells in the human body performing variety of functions from digestion to pumping blood. Surprisingly, these functions are orchestrated by a somewhat identical 2 meters of DNA tightly folded in their 10 nanometer wide nucleus. Thanks to research by us and others, we now know that the spatial organization of genomes inside their nucleus can influence its function. ​We develop and apply innovative genomics technologies (e.g. 4C and Hi-C​) to interrogate this structure​ and​ further integrate ​our results with transcriptomics and epigenomics data to extract new insights about this complex mechanism​. We recently​ extended these approaches to simultaneously assess 3D​ DNA interactions that occur between multiple genomic loci in single-alleles of ​the DNA. Diverse projects are available to further optimize ​existing (or develop new​) analytical tools ​to ​advance our understanding​ of this fascinating system​

Download the PDF file with the detailed description of all projects

Master projects overview-2

For more information and to apply please contact:

Bioinformatic re-assembly of highly polymorphic plant resistance gene clusters


Plant resistance genes encode for receptors that recognize pathogen molecules and trigger an effective immune response. In plant genomes resistance genes are often clustered and highly polymorphic between lines of the same species. This means that the number and DNA sequences of resistance genes is highly variable making it impossible to easily compare these regions between lines. We are now using targeted locus amplication (TLA) followed by NGS to collect sequence reads of these regions. The challenge now is to assembly these reads into correct gene clusters. For this project you will start with Illumina reads of TLA samples and a reference genome. As simple mapping of reads to the reference will not work you will need to make a hybrid approach between mapping and de novo assembly followed by annotation. A method for this does not exist yet, so needs to be develop in the proposed project. A challenging and interesting project that is closely linked to the lab research of our Plant-Microbe Interactions group