Jingyuan Fu, PhD
BSc, 1995, in Biochemistry, Nanjing University, China
MSc (with distinction), 2003, in Bioinformatics, Wageningen University, the Netherlands
PhD thesis (cum laude): Bioinformatics for Genetical Genomics: Novel Experimental Design and Algorithms,
ISBN: 978-90-367-3081-5, University of Groningen, 2007.
- Appointed Associate Professor (February 2015)
- VIDI grant awarded (May 2014) for proposal "Understanding the causal relationships between the host genome, microbiota and lipids"
- Fu et al. (2015) paper, “Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids” recognized as a Circulation Research’s Best Manuscripts of 2015. The paper received massive worldwide press coverage, more.
- See also an article on my work (in Dutch)
My research interests lie in systems genetics, which seeks to understand complex biological systems by integrating systems biology with genetics. I perform integration analyses that combine multidimensional “omics” data and genetic variations. This leads to statistical models and networks, and eventually to causal inference from genotype to phenotype in complex traits and diseases. For example, I have been working on the genetic regulation of gene expression in different model organisms and humans, and assessing the plasticity of this regulation under different conditions (patients or controls) and in different tissues or cell types.
My research shows that trait-associated SNPs are more likely to have an effect on gene expression and that their effects are also more likely to be tissue-dependent. Further, I perform systematic analyses across multidimensional “omics” levels and have observed that only a handful of genetic variations are detectable at the phenotype level. The largest fraction of genetic variants and molecular variants have very small effects that are undetectable at current sample sizes. This observation is in line with findings from genome-wide association studies (GWAS) that show that common variants with (very) small effects explain most of the disease or trait heritability.
In June 2008, I joined Prof. Cisca Wijmenga’s group as a post-doc in the Department of Genetics, at the University Medical Center Groningen (UMCG). My aim was to shorten the road from GWAS study to causal gene identification by integrating evidence from multiple levels, including data from microarray experiments, protein-protein interactions, metabolic pathways and from the literature. In 2009, I was awarded a NWO VENI grant to continue pursuing this systems genetics work.
In May 2014, I was awarded a VIDI grant to work on improving our understanding of the causal relationships between the human host genome, the microbiome and lipids. The goal of this project is to identify the relationship of the gut microbiome with abnormal lipid profiles and predisposition to disease within a unique population cohort, Lifelines-DEEP. This is a general population cohort of 1,500 individuals aged 18 to 80 years old for whom extensive genetic, phenotypic and health-related data has been collected. To date we have published research relating the microbiome composition to blood lipid levels and examining the microbiome composition and function in relation to health and environmental factors. We are now continuing this research with a focus on the influence of genetic background on the microbiome.
I am currently supervising 5 PhD students:
- Biljana Atanasovska (2013-2018) working on the role of non-coding RNAs in non-alcoholic fatty liver diseases
- Soesma Jankipersadsing (2015-2018) working on the impact of gut microbiome on gut health
- Lianmin Chen (2017-2022) studying the role of gut microbiome in cardiometabolic disorders
- Sanne Garmaeva (2017-2021) studying the evolution of the gut ecosystem during the first year of life
- Marwah Doestzada (2017-2021) studying the gut-liver axis: microbiome’s role in the aetiology of non-alcoholic fatty liver disease
and 2 postdocs:
- Alexander Kurilshikova (2015- ) on genetic and environmental effect on microbiota composition
- Dasha Zhernakova (2016- ) on how individual variation in cardiovascular disease-related proteins is driven by genetics and gut microbiome
- Naishi Li (2011-2013) PhD awarded for thesis on "Novel mechanisms for prevention and treatment of type 2 diabetes"
- Marijke van der Sijde (2012-2016) data analysis on the genetic variation in transcriptome
- Young Investigator award (€183k, 2016) from the Dutch Heart Foundation (CVON), co-PI with Sasha Zhernakova
- NWO Aspasia grant (€100k, 2015)
- NWO-VIDI (personal grant, €800k, 2014) "Understanding the causal relationships between the host genome, microbiota and lipids", PI
- BBMRI-complement project (€51k), July 2013–Dec 2014, co-PI
- NWO-VENI (personal grant, €250k), July 2010–July 2013, PI
- Dutch Digestive Diseases Foundation (MLDS) grant (€125k) 2011, co-applicant
- Chinese Government Award for Outstanding Student Abroad, 2006
- Netherlands Fellowship Program, Aug 2001-Feb 2003
- 2nd People’s Prize for the Best Student, Nanjing University, China, awarded in both 1992 and 1994
See all my papers in GoogleScholar; *shared first author
Atanasovska B, Fu J The non-coding genome in cancer Non-coding RNA Investigation 2018;2(1)
- Kurilshikov A, Wijmenga C, Fu J, Zhernakova A Host genetics and gut microbiome: challenges and perspectives Trends in immunology 2017;38(9):633-647
- Atanasovska B, Rensen SS, ... Hofker MH†, Fu J A liver-specific long non-coding RNA with a role in cell viability is elevated in human non-alcoholic steatohepatitis. Hepatology 2017;66(3):794-808
- Bonder MJ, Kurilshikov A, ... Fu J#, Zhernakova A# (). The effect of host genetics on the gut microbiome. Nature Genetics 2016;48(11):1407-1412
- Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, … Fu J. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 2016;352(6285):565–569.
- Falcony G, Joossens M, Vieira-Silva S, … Fu J, … Raes J. Population-level analysis of gut microbiome variation. Science 2016;352(6285):560–564.
- Wang Z, Koonen D, Hofker M, Fu J. Gut microbiome and lipid metabolism: from associations to mechanisms. Current Opinion in Lipidology 2016;27(3):216-224.
- Fu J, Bonder MJ, Cenit MC, Tigchelaar EF, Maatman A, Dekens JA, Brandsma E, Marczynska J, Imhann F, Weersma RK, Franke L, Poon TW, Xavier RJ, Gevers D, Hofker MH, Wijmenga C, Zhernakova A. The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids. Circ Res. 2015;117:817-824. Best paper award
- Fu J, Hofker M, and Wijmenga C. Apple or Pear: Size and Shape Matter. Cell Metab. 2015;21:507–508.
- Brandsma E, Houben T, Fu J, Shiri-Sverdlov R, Hofker MH. The immunity-diet-microbiota axis in the development of metabolic syndrome. Current opinion in lipidology 2015;26(2):73-81.
- Hofker MH, Fu J, and Wijmenga C. The genome revolution and its role in understanding complex diseases. Biochim. Biophys. Acta 2014;1842:1889–1895.
- Li N, van der Sijde MR, Study LC, Bakker SJL, Dullaart RPF, van der Harst P, Gansevoort RT, Elbers CC, Wijmenga C, Snieder H, et al. Pleiotropic effects of lipid genes on plasma glucose, HbA1c and HOMA-IR levels. Diabetes 2014;63:3149–3158.
- Van der Sijde MR, Ng A, and Fu J. Systems genetics: from GWAS to disease pathways. Biochim. Biophys. Acta 2014;1842:1903-1909.
- Kumar V, Westra HJ, Karjalainen J, Zhernakova DV, Esko T, Hrdlickova B, Almeida R, Zhernakova A, Reinmaa E, Võsa U, Hofker MH, Fehrmann RS, Fu J, Withoff S, Metspalu A, Franke L, Wijmenga C. Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. PLoS Genet. 2013;9(1):e1003201. Free PMC article
- Fransen K, Mitrovic M, van Diemen CC, Thelma BK, ... Fu J, Nolte I, Weersma RK. Limited evidence for parent-of-origin effects in inflammatory bowel disease associated loci. PLoS One. 2012;7(9):e45287. Free PMC article
- Prins BP, Lagou V, Asselbergs FW, Snieder H, Fu J. Genetics of coronary artery disease: Genome-wide association studies and beyond. Atherosclerosis. 2012 Nov;225(1):1-10.
- Fu J, Wolfs MG, Deelen P, Westra HJ, Fehrmann RS, Te Meerman GJ, ... Jansen RC, Hofker MH, Wijmenga C, Franke L. Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. PLoS Genet. 2012;8:e1002431. Free PMC article
- Wain LV, Verwoert GC, O'Reilly PF, Shi G, ... Fu J, et al. Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure. Nat Genet. 2011;43:1005-11. Free PMC article
- Fu J*, Festen EA*, Wijmenga C. Multi-ethnic studies in complex traits. Hum Mol Genet. 2011;20:R206-13. Free PMC article
- Fehrmann RS, Jansen RC, ... Fu J, ... Wijmenga C, Te Meerman GJ, Franke L. Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS Genet. 2011 Aug;7(8):e1002197. Free PMC article
- Sotoodehnia N, Isaacs A, de Bakker PI, ... Fu J, et al. Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nat Genet. 2010;42:1068-76.
- Fransen K, Visschedijk MC, van Sommeren S, Fu JY, ... Wijmenga C, van Diemen CC, Weersma RK. Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease. Hum Mol Genet. 2010 Sep 1;19(17):3482-8. Free article
- Fu J*, Keurentjes JJ*, ... Breitling R, Jansen RC. System-wide molecular evidence for phenotypic buffering in Arabidopsis. Nat Genet. 2009;41:166-7. Faculty 1000 Biology: MUST READ.
- Fu J, Swertz MA, Keurentjes JJ, Jansen RC. MetaNetwork: a computational protocol for the genetic study of metabolic networks. Nat Protoc. 2007;2:685-94.
- Keurentjes JJ*, Fu J*, Terpstra IR*, ... Jansen RC. Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc Natl Acad Sci USA. 2007;104:1708-13.
- Keurentjes JJ*, Fu J*, de Vos CH*, ... Jansen RC, Vreugdenhil D, Koornneef M. The genetics of plant metabolism. Nat Genet. 2006;38:842-9. Faculty 1000 Biology: MUST READ.
Invited presentations at international conferences since 2015
- Keynote speaker, International Society for the Study of Fatty Acids and Lipids (ISSFAL) 23-31 May 2018, Las Vegas, USA. "The role of the gut microbiome in lipid metabolism"
- Keynote speaker, Benelux Bioinformatics Conference, 13-14 Dec 2017, Leuven, Belgium. “Genetic and microbial effects on circulating levels of proteins and metabolites is linked to host health"
- Keynote speaker, Genome Biology Satellite meeting, Queenstown Research Week, 3-4 Sept 2017, Queenstown, New Zealand. “Our genomes: the interaction of genome and metagenomics paves the way towards personalized medicine”
- Keynote speaker, Symposium on Human Microbiome Interactions. Auckland University, 28 Aug 2017, Auckland, New Zealand. “Microbial impact on circulating levels of proteins and metabolites is linked to host health”
- Oral presentation at European Society of Human Genetics, 25-30 May 2016, Copenhagen, Denmark. “Systems genetics and metagenome analysis on circulating proteins”
- Invited speaker at the Gut Microbiome Session, American Heart Association Scientific Sessions 2016. 12-16 Nov 2016, New Orleans, USA. “Gut Microbiome in CVD”
- Invited speaker at the Best Circulation Research Session, American Heart Association Scientific Sessions 2016. 12-16 Nov, New Orleans, USA. “Gut microbiome contribute substantial proportion of variation in blood lipids”
- Invited speaker at 84th European Atherosclerosis Society 2016. 29 May-1 June, Innsbruck, Austria. “Developing Therapeutic Microbiome in Cardiovascular Diseases”
- Invited speaker at Heart Failure Association Winter Research Meeting, 20-23 Jan 2016. Les Diablerets, Switzerland. “Developing Therapeutic Microbiome in Cardiovascular Diseases”
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