Prof. Dr. Yang Li participates in the RESIST study.
|My Research Interest in RESIST|
In RESIST, we focus on studying how genetic variation affects molecular and immune phenotypes such as gene expression, metabolites and cytokine responses to stimulations. We develop computational methods and algorithms for fully exploit high-throughput datasets from the most recent profiling technologies, e.g., causal inference and deconvolution of the overall genetic regulation effects of gene expression into relevant cell types. We also integrate large multi-omics data sets and immune profiling of patient to unravel the genotype-phenotype map on a genome- wide scale and built computational models for predicting immune functions and disease risk.
Our aim is to reveal the host genetic risk factors and their downstream molecular pathways as well as to improve the identification of at risk patients, which are crucial to make progress in understanding and treating infectious diseases in an individualized manner.
Prof. Li about her scientific work
Prof. Dr. Yang Li – Curriculum Vitae
Since 2019 Department head of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine, Helmholtz Centre for Infection Research & Hannover Medical School
Undergraduate and Postgraduate Training
1992 – 1996 Bachelor of Science, Chemistry, Hunan University, China (Entrance Exam Exempted)
1996 – 1999 Master of Science, Analytical Chemistry, Hunan University, China (Entrance Exam Exempted)
2005 – 2010 Ph.D. student, Groningen Bioinformatics Centre, University of Groningen, The Netherlands
Academic and Research Posts
1999 – 2001 Researcher & Assistant Lecturer, Hunan University (China)
2001 – 2005 Researcher & Lecturer, permanent position, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University (China)
2010 – 2013 Postdoc, fixed term, Groningen Bioinformatics Centre (GBiC), University of Groningen, Groningen, The Netherlands
2013 – 2019 Principal Investigator, Assistant Professor, fixed term, Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
2019 Head of Department of Computational biology for individualized medicine, Helmholtz Centre for Infection Research, Centre for Individualised Infection Medicine, Hannover, Germany,
Principal Investigator, Hypatia Tenure Track Assistant Professor, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
Other Scientific Roles
2009 – 2013 Member of the EU FP7 PANACEA consortium on the systems genetics of cancer.
2013 Member of the Human Functional Genomics consortium on integrating environmental and genetic factors with immune responses to decipher inflammatory disease pathogenesis.
2017 Member of the Netherlands Organ-on-Chip Initiative, Dutch Organization for Scientific Research (NWO), The Netherlands
2019 Member of the Scientific Advisory Board of the Milieu Interieur Consourtium, France
Awards and Prizes
2011 Dutch Bioinformatics Young Investigator Award, Netherlands Bioinformatics Centre (One winner/year)
2013 VENI Grant: Dutch Organization for Scientific Research (NWO) under its Innovational Research Incentives Scheme for „remarkable and original talent for conducting innovative scientific research“ targeting researchers who have recently gained their PhD (top 10%)
2014 Qingtian Award for Outstanding Chinese researcher in The Netherlands
2016 Off-Road Grant: the Netherlands Organisation for Health Research and Development (ZonMw) for “challenging young talented researchers to enforce unexpected breakthroughs in biomedical and/or health research.” (top 6%)
2018 Renowned Overseas Professors by Guangdong Pharmaceutical University
2018 Hypatia Grant: Radboud University Medical Centre, the Netherlands (top 3%)
10 Selected Publications (of > 67 original publications)
Bakker, O. B., Aguirre-Gamboa, R., Sanna, S., Oosting, M., Smeekens, S. P., Jaeger, M., Zorro, M., Võsa, U., Withoff, S., Netea-Maier, R. T., Koenen, H. J. P. M., Joosten, I., Xavier, R. J., Franke, L., Joosten, L. A. B., Kumar, V., Wijmenga, C., Netea, M. G. & Li, Y. Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses. Nature Immunology 19, 776–786 (2018).
Li, Y., Oosting, M., Smeekens, S. P., Jaeger, M., Aguirre-Gamboa, R., Le, K. T. T., Deelen, P., Ricaño-Ponce, I., Schoffelen, T., Jansen, A. F. M., Swertz, M. A., Withoff, S., van de Vosse, E., van Deuren, M., van de Veerdonk, F., Zhernakova, A., van der Meer, J. W. M., Xavier, R. J., Franke, L., Joosten, L. A. B., Wijmenga, C., Kumar, V. & Netea, M. G. A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans. Cell 167, 1099-1110.e14 (2016).
Aguirre-Gamboa, R., Joosten, I., Urbano, P. C. M., Molen, R. G. van der, Rijssen, E. van, Cranenbroek, B. van, Oosting, M., Smeekens, S., Jaeger, M., Zorro, M., Withoff, S., Herwaarden, A. E. van, Sweep, F. C. G. J., Netea, R. T., Swertz, M. A., Franke, L., Xavier, R. J., Joosten, L. A. B., Netea, M. G., Wijmenga, C., Kumar, V., Li, Y. & Koenen, H. J. P. M. Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits. Cell Reports 17, 2474–2487 (2016).
Li, Y., Oosting, M., Deelen, P., Ricaño-Ponce, I., Smeekens, S., Jaeger, M., Matzaraki, V., Swertz, M. A., Xavier, R. J., Franke, L., Wijmenga, C., Joosten, L. A. B., Kumar, V. & Netea, M. G. Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi. Nat Med 22, 952–960 (2016)
van der Velde, K. J., de Haan, M., Zych, K., Arends, D., Snoek, L. B., Kammenga, J. E., Jansen, R. C., Swertz, M. A. & Li, Y. WormQTLHD–a web database for linking human disease to natural variation data in C. elegans. Nucleic Acids Res. 42, D794-801 (2014)
Li, Y., Tesson, B. M., Churchill, G. A. & Jansen, R. C. Critical reasoning on causal inference in genome-wide linkage and association studies. Trends Genet. 26, 493–498 (2010).
Gerrits, A., Li, Y., Tesson, B. M., Bystrykh, L. V., Weersing, E., Ausema, A., Dontje, B., Wang, X., Breitling, R., Jansen, R. C. & de Haan, G. Expression quantitative trait loci are highly sensitive to cellular differentiation state. PLoS Genet. 5, e1000692 (2009).
Li, Y., Swertz, M. A., Vera, G., Fu, J., Breitling, R. & Jansen, R. C. designGG: an R-package and web tool for the optimal design of genetical genomics experiments. BMC Bioinformatics 10, 188 (2009)
R. Breitling, R., Li, Y., Tesson, B. M., Fu, J., Wu, C., Wiltshire, T., Gerrits, A., Bystrykh, L. V., de Haan, G., Su, A. I. & Jansen, R. C. Genetical genomics: spotlight on QTL hotspots. PLoS Genet. 4, e1000232 (2008).
Li, Y., Alvarez, O. A., Gutteling, E. W., Tijsterman, M., Fu, J., Riksen, J. A. G., Hazendonk, E., Prins, P., Plasterk, R. H. A., Jansen, R. C., Breitling, R. & Kammenga, J. E. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet. 2, e222 (2006).