Aalt-Jan van Dijk's research focuses on the development and application of machine learning methods in the life sciences. In close collaboration with colleagues working on specific biological questions, he deploys these methods to analyze large data sets generated within research on molecular aspects of biology. These include data obtained from genomics, proteomics and metabolomics, for example. An important aspect of the research is how machine learning models can be made more interpretable. In this way, more insight can be gained into biological systems, such as gene regulation networks or the activity of enzymes. In addition, making the models more interpretable can also help design interventions that can be implemented in the lab. An example of the latter is mutating proteins in such a way that their interaction pattern is modified very specifically. In his research, Van Dijk demonstrates the power of this type of collaboration between data analysis and experimental research for solving biological questions.

Collaboration within the Faculty of Science

The research group that Van Dijk will lead is the Biosystems Data Analysis (BDA) group of the Swammerdam Institute for Life Sciences (SILS). He wants to strengthen the collaboration between this group and other research groups at the Faculty of Science. In terms of methodology development, he hopes for even closer cooperation with various groups at the Informatics Institute. Regarding the investigation of biological and biochemical applications, Van Dijk sees many opportunities for joint projects, both with colleagues at SILS and with researchers from other institutes, such as the Van 't Hoff Institute for Molecular Sciences.

Van Dijk will contribute to the teaching of various courses in which bioinformatics and the analysis of molecular (omics) data play a role. This is in particular the case at the bachelor and master of biomedical sciences, and at the master's program Bioinformatics and Systems Biology (joint degree UvA/VU). In addition, he will supervise undergraduate and graduate students in research projects within SILS.

About Aalt-Jan van Dijk

Van Dijk received his PhD from Utrecht University in 2006 with a research focus on predicting the structure of proteins that bind to each other using protein docking. He then worked for several years as a Bioscience researcher at Wageningen University and Research (WUR). From 2016, he was appointed associate professor at WUR where he then worked as associate professor of Bioinformatics from 2021.

As (co-)author of ~100 peer-reviewed publications, Van Dijk has made significant contributions to his field. These include the development of methods for, for example, predicting the function of genes using machine learning, as well as applications of the methods to concrete biological questions.  In addition to a NWO Veni grant, Van Dijk has acquired several projects, for example from NWO-TTW or NWO-M2. He also participates in the recently launched NWO-LTP program CropXR. Van Dijk's commitment to teaching and course development is evidenced by his extensive experience in developing and teaching courses related to data science and machine learning, at the undergraduate, graduate and PhD levels. He has also been research coordinator in the graduate school Experimental Plant Sciences since 2023.