Meet UBC Principal Investigator Lucas Kaaij

Meet UBC Principal Investigator Lucas Kaaij

Supporting the collaborative spirit of the UBC, dr. Lucas Kaaij has recently joined our community as Principal Investigator. In this interview, Lucas introduces us into his research field and the pivotal role of bioinformatics in unravelling its complexities.

Working as an assistant professor at UMC Utrecht’s Center for Molecular Medicine, Lucas Kaaij and his team study how the organization of the 3D genome is regulated and how its architecture impacts the regulation of gene expression. Lucas recently joined the UBC as Principal Investigator and will host a UBC Seminar on the 29th of January, sharing his most recent bioinformatics-related research.

"Bioinformatics has shown to be key for obtaining insight from the sequencing reads in an efficient and sensible manner."

Lucas Kaaij

Why do we need bioinformatics to understand the 3D genome?

The research field of 3D genome organization has evolved rapidly over the last decade. This is largely driven by the implementation of massive parallel sequencing based techniques to the field. The reduction in sequencing costs per base has resulted in the possibility to map 3D genome organization at ever increasing resolution at genome-wide scale. The opportunity to generate millions or even billions of sequencing reads possessing information on DNA folding in the nucleus also presents us with the next challenge of distilling this information. Bioinformatics has shown to be key for obtaining insight from the sequencing reads in an efficient and sensible manner.  

 

How do you incorporate bioinformatics in your research?

In my laboratory we aim to understand how 3D genome organization is regulated on a molecular level and how DNA folding in turn regulates cellular homeostasis while allowing differentiation to occur at the same time. We use a variety of genomics techniques, e.g. ChIP-seq,HiC, RNA-seq and NOMe-seq. Often we use them in combination with genetic perturbation or throughout differentiation with the aim to understand how 3D genome organization is regulated and/or changed.

All these genomics techniques result in a lot of data that simply cannot be analysed by hand. So, in practice in my laboratory, we spend approximately 50% of our time performing experiments and the other 50% we analyse the sequencing reads using multiple bioinformatic tools. For instance, through bioinformatic analysis we determine which pieces of the linear genome are close together in 3D space.

Are you actively looking for collaborations at the moment?

Currently, we don’t have a specific question which requires expertise from a particular discipline. However, having written this, I believe that many of the constructive feedback I received in the past came from people with different backgrounds. Often they approach problems from a different perspective and could help identify opportunities I was not yet aware of.

What are you looking forward to most as a PI of the UBC?

By actively participating in the UBC community, I hope to obtain more insight and get inspired by interesting research in the wider field of bioinformatics in Utrecht. The different backgrounds of people within the UBC make it a great platform for sharing my own research. This will hopefully result in interesting discussions, the identification of novel research opportunities and new collaborations.

Lastly, we are also actively searching for a bioinformatician to tackle questions related to genomics and proteomics. So feel free to contact me if you are interested in our research!

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