Lude Franke
Professor of functional genomics. 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
Assistant professor. I started a bachelor in Biomedical Sciences at the Radboud University in Nijmegen, after which I continued with a research master in Oncology at the VU university in Amsterdam. Driven by my interest in epigenetics and gene regulation and inspired by the innovative approach that her lab was pursuing (epigenetic editing—targeted rewriting of epigenetic marks), I started my PhD in the lab of Marianne Rots in 2012 at the University Medical Center Groningen. I then successfully adapted this approach to study the function of mitochondrial epigenetics, and received my PhD in 2016 cum laude. After my PhD, I joined the functional genomics group of Lude Franke as a postdoc and since 2021 as assistant professor to study how genetics impacts gene expression, its regulation, and the immune response. For this, I have been setting up various single-cell (scRNA-seq, multiomics, spatial) and high-throughput experimental (CRISPR-coupled single-cell sequencing, MPRA) read-outs in the lab. I believe it is the combination of large-scale population-based single-cell QTL meta-analyses (as I am conducting through my leadership within the sc-eQTLGen consortium) coupled to these high-throughput experimental approaches that allow us to functionally interrogate the consequences of genetic variation and cell-to-cell heterogeneity.
Marc Jan Bonder
Postdoc. 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 Skłodowska-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.
https://www.linkedin.com/in/marcjanbonder/
Jackie Dekens
Project manager. My motivation is to apply medical-scientific knowledge for the societal benefit. Experienced in launching multidisciplinary innovative complex projects I currently coordinate UMCG-wide programs LifelinesNEXT birth cohort and the pharmacogenetic passport programme. I am working at the dept of genetics and the UMCG Innovation Center as well.
I joined UMCG in 2011 with ample experience in the pharmaceutical world. Upon obtaining my pharmacy degree in 1990, after working for a short time in a public pharmacy, I got involved in pioneering in post marketing surveillance as a coordinator at REB-Groningen, later known as the Netherlands Pharmacovigilance Centre LAREB. From 2002 on I was coordinator in postdoctoral education (Pharmacotherapy and pharmacy game GIMMICS) at the University of Groningen (Dept of Pharmacotherapy & Pharmaceutical Patient Care). As a Liaison Pharmacist in Proeftuin Farmacie Groningen I also took up the implementation of newly regionally developed pharmacotherapeutical guidelines.
Martijn Vochteloo
PhD student. I have a Bachelor’s in Bioinformatics and a Master’s in Data Science for Life Sciences from the Hanze University of Applied Sciences in Groningen, The Netherlands. In 2020 I started my PhD at the Functional Genomics Group. My research focuses on understanding how genes in the human brain are regulated in different cellular contexts.
Roy Oelen
PhD student. My background is bio-informatics (B.Sc) and software development. After a brief stint working as a programmer in the software industry, I refocussed 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.
Twitter: https://twitter.com/OelenRoy
Dan Kaptijn
PhD student. I have a background in Biology (BSc) and Bioinformatics and Systems Biology (MSc) which I studied at Liverpool John Moores University, and the VU Amsterdam respectively. In 2022 I started my PhD at the Functional Genomics group, my research focus is on combining single-cell data in a federated manner.
Anne van Ewijk
Bioinformatician. I studied bioinformatics at the Hogeschool Arnhem Nijmegen (HAN) and gratuated in 2019. After working for a year (at Vartion), I started the master Data Science for Life Sciences at the Hanzehogeschool in Groningen (gratuated in 2022) . During this master I did my graduation internship within the Functional Genomics group and continued working as a data analyst on various COVID projects. I mainly look at the difference between people who have Long COVID and people who have had COVID but not Long COVID.
Irene van Blokland
MD/PhD student. After completing my bachelor in cellular and molecular biology at the Norwegian University of Science and Technology and my bachelor in medicine at the University of Groningen, I currently combine my masters in medicine with doctoral research as MD-PhD student.
I study the role of inflammation on individual cell level in ischemic heart disease. Through a multi-omic approach and the use of state-of-the art techniques on various tissues I aim to generate a multidimensional understanding of the inflammatory response. Using this, I aim to increase our current understanding of ischemic heart disease which can be used to identify new therapeutic targets.
Alumni
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
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
Harm-Jan Westra
Staff scientist. 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
Staff scientist. 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.
Carlos Urzua Traslaviña
Postdoc. I trained as a Medical Doctor before changing topics and graduating MRes in Bioinformatics at the University of Groningen. Then I started my PhD at the group of Rudolf Fehrmann (UMCG) where I developed methods that leverage mRNA expression data to predict gene function, and measure the downstream effects of copy-number alterations in cancer. I also participated in the development of the visualization for the ESMO-Measure of Clinical Benefit Scale which explains visually to a non-expert the expected clinical benefit of an anti-cancer treatment. I am currently working at the Functional Genomics group to study the downstream effect of non-coding mutations in cancer. I greatly enjoy working with new (machine learning) methods and to create visual art from data.
https://nl.linkedin.com/in/carlos-urzua-47640b65
Pauline Lanting
PhD student. I obtained my bachelor and master in pharmacy at the University of Groningen. After a short period working in community pharmacy as a registered pharmacist, I joined the Genetics department of the University Medical Center Groningen in 2016. Subsequently, I started my PhD with the Functional Genomics Group in 2018. My research has a focus on pharmacogenomics in patient and population cohorts.
Tijs van Lieshout
PhD Student. My passion for data analysis began during my undergraduate studies in Bioinformatics at the HAN University of Applied Sciences in Nijmegen. I later pursued this interest further by completing a Master's degree in Data Science for Life Sciences at the Hanze University of Applied Sciences in Groningen. During my studies, I have had the pleasure to work on projects across a range of topics within bioinformatics. Within the Functional Genomics group, I am studying non-coding somatic mutations and their functional downstream consequences in cancer.
https://tivali.org/
Robert Warmerdam
PhD student. Enthusiastic about biology and computer science, I started studying bioinformatics at the Hanze University of Applied Sciences in Groningen in 2015. The various projects and internships I successfully completed made me want to develop my skills in method development and data analysis in the world of bioinformatics. To pursue this plan, I 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. Secondly, I started working on the second phase of the eQTLGen consortium. In this phase, we aimed to perform a large-scale genome-wide trans-eQTL meta-analysis. In addition, 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. In September 2021, I officially started as a PhD student. Currently, I am continuing to work on both pharmacogenetics and performing genome-wide eQTL meta-analyses within the eQTLGen consortium.
Maryna Korshevniuk
PhD student. 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
Research Technician, I studied Biology and Medical Laboratory Research at the Hanze Hogeschool in Groningen and did my thesis in Oslo University Hospital. My job consists of conducting research experiments related to the wet lab such as sc-multiomics, sc-genomics and MPRA.
Marjolein Dijkema
Research Technician, I studied biotechnology in my bachelor's and specialized in medical biotechnology during master’s, both at Wageningen University. My master’s internship was at the Tokyo University of Agriculture and Technology, Japan where I lived for a year. My work here in the group mainly focuses on establishing systems expressing CRISPR-Cas9 base-editing activity and the generation of single cell RNA sequencing data.