Lude Franke
I studied biomedical sciences at Utrecht University, and started as a PhD student in 2002 at the University Medical Center Utrecht. I subsequently did a postdoc at QMUL (London) and started as assistant professor at the University Medical Centre Groningen. Since 2019 I am a full professor, working on the development and application of novel statistical algorithms to large scale genomics data. I am also a graphical designer.
Monique van der Wijst
My research examines how (non-genetic) cell-to-cell variation shapes gene expression, its regulation, and the immune response. I secured a NWO Medium Investment grant (2018) to establish the required single?cell infrastructure, as well as several personal awards, including a NWO Veni (2019) and Vidi (2023), to pursue these research directions. To extend this program to cell–cell communication and spatial regulatory niches, I received a collaborative KWF Exploration Grant (2025), enabling investigation of the immune interactome in B?cell lymphomas. To capitalize on advances in single?cell technologies, and international initiatives such as the Human Cell Atlas, I founded the single?cell eQTLGen consortium (2018). Together with consortium partners and my team of six PhD students, we are now developing high-throughput experimental and computational strategies to reconstruct GRNs from single-cell data.
Marc Jan Bonder
I studied bioinformatics at the Hanze University Groningen, afterwards I did a masters in bioinformatics at the VU Amsterdam. I obtained my PhD (cum laude) in Groningen at the UMCG, under supervision of Lude Franke, Alexandra Zhernakova and Cisca Wijmenga. After my PhD I was awarded a Interdisciplinary Postdoc fellowship, funded by EMBL & Marie Sklodowska-Curie Actions to do a Postdoc at EMBL-EBI and EMBL to work in the group of Oliver Stegle. After my PostDoc at EMBL/EMBL-EBI I worked as a team leader at the DKFZ in Heidelberg in the division of Computational Genomics and Systems Genetics. Currently I’m a Postdoc in the functional genomics lab, where I’m working on single cell genomics projects and I’m co-leading the sc-eQTLGen effort.
Roy Oelen
My background is bio-informatics (BSc) and software development. After a brief stint working as a programmer in the software industry, I refocused my efforts on research at the University Medical Centre Groningen. First working on innovation projects at the Intensive Care Unit, and now as a bio-informatician and PhD student at the Genetics department. I am currently involved in research using single-cell transcriptomics data to better understand the contexts in which genetic variation can increase the risk of, or severity of disease.
Dan Kaptijn
I have a background in Biology (BSc) and Bioinformatics and Systems Biology (MSc) from Liverpool John Moores University, and the VU Amsterdam respectively. In 2022 I started my PhD at the Functional Genomics group. I have worked a lot with the single-cell eQTLGen consortium, where we have fostered collaborations with other research groups working with PBMC single-cell data. This consortium is allowing us to investigate research questions at a scale that was not possible before. My research now focusses on utilizing this data to identify complex relationships not only between genes but also between different tissues and to what extent these relationships are shaped by our genetic DNA sequence.
Lilia Ouadah
I graduated with a PharmD degree from Paris-Saclay University and later completed a Master’s degree in Bioinformatics at Université Paris Cité. During my studies, I worked on several genomics and bioinformatics projects in Hungary and South Korea, including RNA-seq, whole-exome sequencing, and EHR-based machine learning. My current PhD research focuses on same-cell single-cell multiomics and mitochondrial DNA sequencing to better understand the molecular mechanisms underlying cell-to-cell variation in innate immune memory. Outside of science, I enjoy discovering new restaurants, cheese, karaoke and running.
Bhavana Kapalli
I have a bachelor’s degree in Biochemistry from Maastricht University and a Master’s degree in Bioinformatics from Boston University. During my studies, I worked on genomics and epigenomics projects related to cancer and neurological disorders. My current PhD research focuses on understanding how Hodgkin lymphoma tumor cells hijack CD4 T cells within the tumor microenvironment using single-cell multiomics and spatial transcriptomics approaches. The goal of my research is to identify novel cell-cell interaction targets that could enable more precise and less toxic therapies for Hodgkin lymphoma patients.
Former Members and Alumni
Jackie Dekens, Project manager
Carlos Urzua Traslaviña, Postdoc
Pauline Lanting, PhD
Martijn Vochteloo, PhD
Anne van Ewijk, Bioinformatician
Marjolein Dijkema, Research Technician
Irene van Blokland, MD/PhD
Dylan de Vries, PhD
Adriaan de Graaf, PhD
Niek de Klein, PhD
Annique Claringbould, PhD
Omar el Garwany, MSc
Juha Karjalainen, PhD
Benjamin Berkhout, MSc
Dasha Zhernakova, PhD
Harm-Jan Westra
I studied Life Science and Technology at the University of Groningen, specializing in medical microbiology, after which I did a MSc Bioinformatics at the Wageningen University. I started my PhD in 2010 in the group of Lude Franke and Cisca Wijmenga, during which I developed several methods to optimize eQTL analysis, and performed an initial federated cis- and trans-eQTL meta-analysis in blood. After graduating in 2014, I continued my research at the Brigham and Women’s hospital, the Broad institute and Harvard Medical School in Boston, US, where I focused on overlapping epigenetic and GWAS signals and finemapping of genetic signals for rheumatoid arthritis and type 1 diabetes. Late 2017, I returned to the functional genomics lab as a staff scientist, where I am currently involved in federated eQTL meta-analysis in blood and brain. Apart from science, I love (making) (electronic) music and watching bad movies.
Patrick Deelen
I started with a bachelor in bioinformatics obtained at the Hanze University Groningen followed by a master in bioinformatics at VU Amsterdam. I then obtained my PhD at the genetics department of the UMCG under the guidance of Morris Swertz, Lude Franke and Cisca Wijmenga. After my PhD I had postdoc positions at the UMCG genetics department and at the UMCU genetics department. Currently I work as a staff scientist at the functional genomics labs of Lude Franke. Here I’m focussed on gene function predictions using gene-expression data. With this I aim to identify disease relevant genes with the final goal to aid in the diagnosis of patients with unknown rare diseases.
Tijs van Lieshout
I first developed an interest in data analysis while completing my undergraduate studies in Bioinformatics at HAN University of Applied Sciences. I then earned a master's degree in Data Science for Life Sciences at Hanze University in Groningen. In the Functional Genomics group, I apply sequence-based models and gene networks to study non-coding somatic mutations and their functional consequences in cancer.
Robert Warmerdam
I am trained in bioinformatics and joined the Functional Genomics Research Group as a scientific programmer in September 2019. During my time as a scientific programmer, I started working on pharmacogenetics and developed Idéfix, which allows us to detect sample mix-ups in bio-banks. More recently, we developed Asterix, a validated pharmacogenetics pipeline to generate pharmacogenetic profiles based on genotyping arrays. Separately, with help from the Lifelines Corona Research Project, I got the chance to perform data analyses and work on papers to gain insight into COVID-19 and the COVID-19 pandemic. My main project throughout the years has been the eQTLGen consortium. In this project, we perform a large-scale genome-wide trans-eQTL meta-analysis. I am currently finalizing the eQTLGen project and wrapping up my PhD thesis.
Maryna Korshevniuk
My background is in biotechnology (B.Sc.) and chemoinformatics (M.Sc.), and now I combine both wet lab and bioinformatics research in the field of single-cell multiomics. As an early stage researcher in TranSYS, my key focus is personalized medicine, and therefore my research is focused on combining single-cell technologies with genomics to better understand biological processes and use them to develop models for personalized medicine.
Jelmer Niewold
I am a PhD student with a background in Biology and Medical Laboratory Research from Hanze University of Applied Sciences in Groningen, where I developed a strong foundation in molecular and cellular laboratory techniques. After completing my thesis at Oslo University Hospital, I now focus on wet-lab approaches in functional genomics. My research involves single-cell multiomics, mitochondrial DNA-based clonal tracing, and massively parallel reporter assays to investigate gene regulation, cellular heterogeneity, and disease-relevant regulatory variation.
Francisco Camões Magalhães
I have a bachelor's and master's degree in Bioengineering from the University of Porto, with a specialization in Biomedical Engineering. I am fascinated by the application of deep learning (DL) to study the non-coding regions of the genome, as well as by the explainable AI techniques that give us insight into the features learned by these models. My PhD project focuses on combining eQTL data and DL models to study and identify non-coding variants that contribute to the development of rare cancers.
Graduated May 6th, 2026
Graduated September 3rd, 2025
Graduated June 27th, 2024
Graduated December 14th, 2022
Graduated 19th January, 2022
Graduated September 13th, 2021
Graduated December 2nd, 2020
MSc internship brain eQTLs
Graduated January 15th, 2018
MSc internship brain sQTLs
Graduated September 12th, 2016
Joost Bakker