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University Medical Center Groningen

Lude Franke, PhD

Head of Research and Education section, Associate professor
Lude Franke, PhD

Lude Franke (lude@ludesign.nl) is a statistical geneticist, working on the development and application of computational algorithms to functional genomics datasets. He has gained funding from ERC, NWO, and a Horizon Grant. He is also a graphic designer (see his PhD thesis design). This chance combination of skills can sometimes make life as a genetics/bioinformatics researcher a bit easier: if you can explain your research visually, more people can understand what you are doing. See a short film explaning his work on DNA (in Dutch) here and an interview with Lude about his work (in Dutch) here.

Students – We are always looking for bright and enthusiastic students. For more about our projects, please visit the Franke lab and Systems Genetics websites.

News

  • Dec 2016: Appointed member of The Young Academy, KNAW, more, see video interview (with English subtitles)
  • Jan 2016: Appointed Head of Research and Education in the Dept of Genetics, UMCG
  • Jan 2015: Awarded the UMCG research prize (€100k)
  • 2014: ERC Starting grant (€1.5m) and NWO-VIDI grant (800k)

For more information about his current research see the Franke lab website.

Curriculum vitae: Full CV (per Sept 2017, including collaborators, grants and prizes, full list of publications)
PhD thesis: Genome-wide approaches towards identification of susceptibility genes in complex diseases. Awarded cum laude, Utrecht University, 2008

Research achievements

My research over the last six years targets the development and application of computational algorithms to functional genomics datasets. The foundation for this work was laid during my PhD (2008, cum laude) when I developed new, cutting-edge computational and statistical methods for conducting genome-wide association studies (GWAS) and reconstructing gene networks using gene expression data.

After my graduation, I took up concurrent post-doc positions in London (Institute of Cell and Molecular Science, Queen Mary University), and Groningen (University Medical Centre Groningen). In London, I worked on the genetics of immune-mediated diseases (i.e. celiac disease) and in Groningen, on the development of methods to identify the effects of GWAS risk-SNPs on gene expression levels (Franke and Jansen, Methods Mol Bio 2009). My post-doc work resulted in a landmark paper (Dubois et al. Nature Genetics 2010) that combined my work in London and Groningen. In this paper we demonstrated that there were many independent genetic risk-variants in celiac disease and that they mostly increase disease-risk by altering gene expression levels.

As senior author, I subsequently developed various computational methods and software to increase statistical power to identify such effects on gene expression (Westra et al. Bioinformatics 2010). By using these methods, I was able to demonstrate that the genetic risk-variants for many other diseases also have an effect on gene-expression levels (Fehrmann et al. PLoS Genetics 2011), and that these genetic variants often affect gene expression levels only in specific cell types (Fu et al. PLoS Genetics 2012, Westra et al. PLoS Genetics 2015). We showed that SNPs also affect the expression levels of many long non-coding genes (lncRNAs, Kumar et al. PLoS Genetics 2013) and that they can affect poly-adenylation of genes (Zhernakova et al. PLoS Genetics 2013).

Through a large-scale, blood eQTL meta-analysis consortium that I initiated in 2010 and that I am currently leading, we then identified downstream (trans-eQTL) effects for over 100 risk-SNPs (Westra et al. Nature Genetics, 2013). We have shown that, by using functional genomics approaches, we can identify previously unknown pathways for many different diseases.

Another considerable focus point is the development of novel methods to reuse publicly available data. We recently integrated gene expression data from 80,000 microarrays to accurately predict gene functions and to gain better insight into cancer (Fehrmann et al. Nature Genetics 2015), developed DEPICT (Pers et al. Nature Communications 2015) to use these predicted gene functions to better interpret GWAS findings, and developed strategies to integrate genetic variation, gene expression and methylation data (my recent last-author papers include Zhernakova et al. Nature Genetics 2017 and Bonder et al. Nature Genetics 2017).

Currently, my group is concentrating on integrating multi-omics datasets, such as conducting large-scale trans-QTL meta-analyses in >30,000 samples, in conjunction with single-cell RNA-seq data (a paper reporting results of our single-cell RNA-seq eQTL work is under review by Nature Genetics), to identify likely causal genes for diseases that might be targetable by drugs, and to help develop computational strategies to increase the diagnostic yield in clinical genetics, by integrating RNA-seq, whole-genome sequencing data, and gene function prediction.

My group currently has 4 PhD students and 2 postdocs; 4 PhD candidates have already graduated (two cum laude).

Selected papers

See all Lude Franke's papers in Google Scholar
His H-index is 63, he has co-authored >173 papers and has >19,000 citations (per Sept 2017)

Laatst gewijzigd:10 juli 2018 12:50