Lab of bioinformatics and computational genomics

Upon graduating in 2004 as a bioscience engineer, I started my doctoral studies funded by Ghent University (BOF) under the guidance of Prof. Sofie Bekaert and Prof. Wim Van Criekinge. Even then, my main focus was aging, and how it may result in diseases such as cardiovascular disease and cancer. To a major extent, this was catalyzed by my involvement in the Asklepios study on successful aging, where we study for example telomere length. Yet, whereas I started as a wet lab scientist, I quickly realized that I preferred to focus on data analysis, ranging from basic epidemiology over omics to pure bioinformatics. Upon successfully completing and defending my doctoral dissertation in 2008, which included papers on telomere biology, metabolomics as well as microarray data analysis, I obtained an FWO postdoc position.

Given the advent of next-generation sequencing, we started doing epigenomics and transcriptomics research, leading to many interesting collaborations with partners all over the world. Having experience with the new omics field, including the development of new data-analytical methods, also opened many career opportunities, and I was awarded a tenure track professor position in 2010. Throughout the 5-year tenure track period, I continued collaborating in many omics studies, began lecturing on the topic in several courses, but also started (together with Prof. Marchal and Prof. Fostier) the interfaculty Master of Bioinformatics program at Ghent University. Having successfully completed the tenure track, I also shifted from pure biomarker oriented omics studies to more challenging fundamental research on how aging and/or other triggers alter our (epi)genome and transcriptome and may lead to disease. This has led to the current research topics:

• The development and application of improved methods to study allele specific expression and its deregulation in disease. We have developed the MAGE framework to screen for (loss of) imprinting, eQTLs and allelic imbalance using solely RNA-seq data and apply this to study cancer and cardiovascular disease.
• The study of the aging genome: how does DNA methylation driven mutations alter our genome and what is the impact on human health and evolution.
• Of course, we continue collaborating with other experts in applied omics studies. Noteworthy are the long-standing collaborations with among others Prof. Manon Van Engeland (Maastricht University), Prof. Bea Wisman & Prof. Ed Schuuring (Groningen University), Prof. Tina Kyndt (Ghent University), Prof. Frank Peelman, Ghent University).
• The longitudinal Asklepios Study on cardiovascular aging, which tracks over 2,500 volunteers from Erpe-Mere-Nieuwerkerke. This is a long-lasting collaboration with Prof. Ernst Rietzschel, Prof. Sofie Bekaert and Mr. Marc De Buyzere (Faculty of Medicine Health Sciences) and many other Asklepios investigators.

Next to being a core investigator of the Asklepios Study, I’m a member of the Bioinformatics Institute Ghent – Nucleotides 2 Networks (BIGN2N), the Cancer Research Institute Ghent (CRIG), and a partner of the Ghent University sequencing facility NXT-GNT.

My research has led to over 80 publications in peer reviewed journals, of which many at the top of their field (e.g. Nature Communications, Nature Reviews Clinical Oncology, Nucleic Acids Research, the Journal of the American College of Cardiology, Aging Cell, European Heart Journal, Hypertension, BMC Medicine, Cancer Research, Clinical Cancer Research).

Koch, A., Jeschke, J., Van Criekinge, W., van Engeland, M., & De Meyer, T. (2019). MEXPRESS update 2019. NUCLEIC ACIDS RESEARCH, 47(W1), W561–W565.

De Meyer, Tim, Nawrot, T., Bekaert, S., De Buyzere, M., Rietzschel, E., & Andrés, V. (2018). Telomere length as cardiovascular aging biomarker. JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY, 72(7), 805–813.

Koch, Alexander, Joosten, S. C., Feng, Z., de Ruijter, T. C., Draht, M. X., Melotte, V., Smits, K. M., et al. (2018). Analysis of DNA methylation in cancer : location revisited. NATURE REVIEWS CLINICAL ONCOLOGY, 15(7), 459–466.

Goovaerts, T., Steyaert, S., Vandenbussche, C., Galle, J., Thas, O., Van Criekinge, W., & De Meyer, T. (2018). A comprehensive overview of genomic imprinting in breast and its deregulation in cancer. NATURE COMMUNICATIONS, 9.