Jingyuan Fu, PhD

Studies

BSc in Biochemistry, Nanjing University, China, 1995.
MSc (with distinction) in Bioinformatics, Wageningen University, the Netherlands, 2003.
PhD (cum laude) for "Bioinformatics for Genetical Genomics: Novel Experimental Design and Algorithms" ISBN: 978-90-367-3081-5, University of Groningen, 2007.

Email

See all my papers in PubMed or in GoogleScholar

Keywords: bioinformatics, genetics, genomics, systems biology, systems genetics

News

• March 2023: Inaugural lecture "The Wonderland of Our Genomes" in honor of her appointment as Professor of Systems Medicine. pdf of lecture
• March 2023: Awarded the 2023 Ammodo Science award for fundamental research. See the UMCG press release for more information.
• October 2022: 'Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome' published in Nature Medicine. See the UMCG press release for more information.
• April 2022: 'Environmental factors shaping the gut microbiome in a Dutch population' published in Nature. See the UMCG press release for more information.
• February 2022: Appointed full Professor of Systems Medicine
• April 2021: Awarded NWO Vici award for Decoding the human genome and metagenome in cardiometabolic diseases
• April 2021: 'The long-term genetic stability and individual specificity of the human gut microbiome' published in Cell. See the UMCG Press release for more information.
• November 2020: Awarded ERC Consolidator Grant for the BugDrug project
• June 2019: 'Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk: A Cross-Sectional Study' was the cover article in Circulation Research.
• February 2015: Appointed Associate Professor
• May 2014: VIDI grant awarded for "Understanding the causal relationships between the host genome, microbiota and lipids"
• 2015: Fu et al. paper, “Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids” recognized as a Circulation Research Best Manuscript of 2015. The paper received massive worldwide press coverage, more.
• See also an article on my work (in Dutch).

Research interests

Decoding the human genome was a huge step forward for scientists hoping to predict an individual’s risk of disease. We will be able to take this a step further if we learn to understand another code – the genetic make-up of our gut microbiome – and to integrate what these two codebooks tell us.

This is an integral component of my long-standing search for ways to improve human health. My research interests lie in systems genetics. I believe that big data will advance medical development at an unprecedented speed, and I harness this potential in my multidisciplinary research on systems genetics. I perform integration analyses that combine human genome, gut microbiome, and multidimensional omics data. This leads to statistical models and networks, and, eventually, to causal inference from genotype to phenotype in complex traits and diseases.

Research group

I am currently supervising 10 PhD students:

• Sergio Andreu Sanchez (2020-2024) studying the impact of the microbiome on immune senescence
• Marwah Doestzada (2017-2021) studying the gut-liver axis: microbiome’s role in the aetiology of non-alcoholic fatty liver disease
• Yue Zhang (2021-2025) studying the microbiome in HIV
• Victoria Palasantzas (2021-2025) studying the impact of short-chain fatty acids on non-alcoholic fatty liver disease
• Isabel Tamargo (2021-2025) working on a liver chip for personalised drug testing
• Shixian Hu (2017-2021, co-supervised by Prof. R. Weersma) working on integrating multi-comics data to understand the genetic factors of inflammatory bowel disease
• Sana Garmaeva (2017-2021, co-supervised with Prof. A. Zhernakova) studying the evolution of the gut ecosystem during the first year of life
• Trishla Sinha (2018-2022, co-supervised with Prof. A. Zhernakova) studying the microbiome in women health
• Johanne Spreckels (2018-2022, co-supervised with Prof. A. Zhernakova) studying the microbiome in breast milk
• Aiser Fernandez (2021-2025, co-supervised with Prof. A. Zhernakova) studying the impact of exposome on microbiome

5 postdocs:

• Alexander Kurilshikov (2015- ) working on genetic and environmental effects on microbiota composition
• Dasha Zhernakova (2016- ) working on how individual variation in cardiovascular disease-related proteins is driven by genetics and gut microbiome
• Lianmin Chen (2021- , part-time postdoc) studying the role of gut microbiome in cardio-metabolic disorders
• Daoming Wang (2021- ) studying the genetic variation of the microbiome
• Angel J. Ruiz Moreno (2022- ) working on predicting microbe-drug interaction using a chemical informatics approach

and one technician:

• Gwen Weijer (2021- ) working on the development of liver-on-a-chip

PhD theses from the group:

• Lianmin Chen “Environment-host-microbe interactions shape human metabolism” (cum laude) on 22 June 2021
• Valerie Collij “The gut microbiota and inflammatory bowel disease” on 3 Feb 2021
• Biljana Atanasovska "Decoding non-coding RNAs in fatty liver disease” on 20 May 2019
• Naishi Li “Novel mechanisms for prevention and treatment of type 2 diabetes” on 11 Dec 2013

Grants awarded

• NWO-VICI (€1.5M, 2021), "Decoding the human genome and metagenome in cardiometabolic diseases", PI
• ERC Consolidator grant (€2M, 2020), "BugDrug: Enhancing efficacy of commonly used drugs by manipulating gut microbiome", PI
• Young Investigator award (€183k, 2016) from the Dutch Heart Foundation (CVON), co-PI with Sasha Zhernakova
• NWO Aspasia grant (€100k, 2015)
• NWO-VIDI (€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 (€250k), July 2010–July 2013, PI
• Dutch Digestive Diseases Foundation (MLDS) grant (€125k) 2011, co-applicant

Major prizes

• 2023 Ammodo Science award for fundamental research
• 2022 China Gut Festival “Scientist of The Year - Fundamental Research” prize
• 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