4 questions with Jeroen De Ridder

Niko: Prof. De Ridder, thank you so much for finding the time to answer our questions. For the benefit of our readers, could you tell us something about yourself? What does your assistant professor position entail?

Prof. De Ridder: I am a PI / Associate professor at the Utrecht University Medical Center focussing on bioinformatics and computational genomics. The application domain is mostly cancer genomics. I started my current position two years ago, after having spent 4 years as an assistant professor at Delft University of Technology. The lab currently consists of about 14 people of which four are focussing on 'bioinformatics as a service'. In this model we aim to provide commodity (standardised) bioinformatics analyses to other researchers in the institute, such as RNA-seq data analysis, variant calling, etc. The other part of the lab is doing 100% research (and a bit of teaching). The current research focus is on machine learning and data integration methods to solve biological questions that can only be solved by a computational or algorithmic innovation. For example, we are working to design classifiers that can predict which cancer patients will benefit a certain treatment from their gene expression profile. In addition, we collaborate with several wet-lab groups to combine data analytics with biological analyses. Our latest work in this regard is a genomics approach to measure multi-component DNA-DNA contacts to unravel genome conformation at the level of single alleles, together with the lab of Wouter de Laat (Hubrecht).

N: How did you get involved with the iSCB/SC and what was your role in it?

DR: I was involved in setting up the Dutch bioinformatics PhD-student community. After we learned that regional student groups were being organised in - you guessed it - regional student groups (RSGs), we decided to connect to that initiative, and call ourselves RSG-Netherlands. This proved to be a very nice stepping stone to the international network of PhD students, and so many of us subsequently became involved in the ISCB-SC. I must admit that - at the time - funding in the Netherlands for bioinformatics was very very good, enabling us to travel to almost all of the ISMB and ECCB editions. As it turned out, meeting people face to face really promotes collaborations, including those for the organisation of student council events. After a while, I was asked to run for the presidency of the global SC (2010). I must say this was a fantastic time, in particular because of the fantastic team we had. I have very fond memories of a executive team meeting (yes, there was even funding for that at the time) in Cambridge, in which we hacked together various policy documents which, as far as I can tell, are still mostly in effect.

N: Was it difficult to find the right balance between student council and your research?

DR: It is very difficult to find the balance between research and extracurricular activities, such as the SC. It is, however, of vital importance that you succeed in finding this balance. The only way in which I was able to find this balance was to build in moments of self-reflection and self-evaluation. Sitting down with an empty sheet of paper and writing down what the progress on various aspects of your career are (your latest manuscript, your teaching duties, the SC, but also personal life), asking yourself the question: are things still progressing in the right direction, and if the answer is no (which is almost always the case on one or a few sub-points) make a concrete plan on how to change your behaviour to improve this. You can only spend your time once, so better make it count. That means you have to learn to say no to certain activities and/or stop certain activities if you predict them to be less fruitful than initially anticipated.

N: Does it make sense for early-career researchers to be involved with the iSCB/SC? To organize and attend meetings such as the ESCS?

DR: Absolutely. I have made many friends, most of which I still talk to on a regular basis. For instance, I recently visited the lab of Nils Gehlenborg at Harvard, with whom I was in the executive team. We are now collaborating on making visualisations of the multi-contact chromatin interaction data. But apart from the positive effect on your scientific career on the long run, I think there should only be one reason to become active and involved in SC-organized events: because it is a lot of fun. How often do you have dinner with 10 other people that literally come from 10 different countries? If that is not enriching your career and your life, I don't know what is.

N: Do you have one tip for young researchers and students in Bioinformatics/Computational Biology?

DR: Stay curious. This holds for the science you do, but also for the people you meet.


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