Associate Professor Ph.D. (2015) Cornell University Current graduate students: Ke Yi (Genetics; 01/2025-) Elijah Sterling (Genetics; co-advised with Dr. Yao Yao; 05/2024-) Lu Wang (Genetics; 01/2024-) Yueqi Lu (Genetics; 01/2024-) Saurav Kumar Choudhary (Bioinformatics; 01/2023-) Susan Adanna Ihejirika (Bioinformatics; 01/2022-) Huifang Xu (Genetics; 01/2022-) Graduated: Shuang Yang (Genetics; 08/2019-08/2024); Yitang Sun (Genetics; 09/2019-05/2024); Michael Francis (Bioinformatics; 06/2019-12/2022) Research Research Areas: Evolutionary Genetics Genomics and Bioinformatics Molecular Genetics Research Interests: My research interest lies in Nutritional Genomics, an interdisciplinary field bridging Nutritional Sciences and Human Genomics. I am interested in identifying genetic variants that historically helped human populations adapt to local diets and currently underlie individual differences in nutrient metabolism and metabolic disease risks. In the long run, I hope to develop statistical methods that integrate genomic information to personalize our dietary recommendations (Personalized Nutrition). Current research topics in my lab include: 1. Genetic adaptation to diet during human evolution (Population Genetics); 2. Evolution of metabolic genes and complex metabolic traits (Comparative and Population Genetics); 3. Genetic basis of metabolic diseases (Quantitative Genetics; Genetic Epidemiology); 4. Gene-diet interaction in metabolic diseases (Quantitative Genetics; Genetic Epidemiology); 5. Molecular mechanism of genetic variants (Molecular Genetics); 6. Bioinformatic analysis of omics data (Bioinformatics); Grants: R01DE035487 NIDCR 03/2026 – 02/2031 Engineered Synthetic Low-Density Lipoprotein Nanoparticles for Enhanced Cancer Immunotherapy in Head and Neck Cancer Role: Co-investigator (PI: Xie) R01CA299080 NCI 03/2026 – 02/2031 Calcium Nanoparticles to Enhance Immuno- Radiotherapy Role: Co-investigator (PI: Xie) R01HL174378 NHLBI 05/2024 – 04/2029 Leveraging metabolomics to identify factors contributing to health disparities in Native Hawaiian individuals Role: Co-investigator (PI: Darst) R01AG076625 NIA 09/2022 – 08/2027 Implications of Metabolic Dysfunction during Thiamine Insufficiency Role: Co-investigator (PI: Zastre) R01AI151139 NIAID 07/2021 – 06/2026 Markers and regulation of regulatory CD8+ T cells during influenza-induced lung immunopathology Role: Co-investigator (PI: Huang) R35GM143060 NIGMS 08/2021 – 05/2027 Gene-Environment Interactions in Human Evolution and Complex Traits Role: Principal Investigator Selected Publications Selected Publications: * indicates co-first authors; ^ indicates co-corresponding authors; names of group members are in bold; # indicates undergraduate trainees; $ indicates high-school students; Xu H, Yu G#, Lu Y, Fuller H, Song S, Shen Y, Chiang CWK, Darst BF, Ye K. Polygenic predisposition modifies the associations of fish oil supplementation with circulating omega-3 fatty acids: a cross-sectional gene-diet interaction study in UK Biobank. Clinical Nutrition. (2026) Ihejirika SA, Stephen E#, Ye K. A variance QTL approach to uncover gene-fish oil supplement interaction loci for 14 circulating unsaturated fatty acid traits. Human Genetics and Genomics Advances. (2026) Barad A, Xu H, Clark AG, Gu Z, Pressman EK, Ye K^, O’Brien KO^. A genetic association study of iron absorption in adults of East Asian or Northern European ancestry from the Iron Genes in East Asian and Northern European Adults Study (FeGenes). The American Journal of Clinical Nutrition. (2026) Xu H*, Sun Y*, Francis M, Cheng CF#, Modulla NTR#, Brenna JT, Chiang CWK, Ye K. Widespread but moderate genetic overlap between circulating polyunsaturated fatty acids and brain disorders. Journal of Lipid Research. (2025) Lu Y, Xu H, Sun Y, Ihejirika SA, Chiang CWK, Darst BF, Song S, Shen Y, Ye K. Gene-diet interaction analysis in UK Biobank identified genetic loci that modify the association between fish oil supplementation and the incidence of dementia. Current Developments in Nutrition. (2025) Wang L, Xu H, Simons RL, Beach SRH, Lei MK, Ong ML, Philibert RA, Mielke MM, Sun Y, Lu Y, Chiang CWK, Darst BF, Ye K. Associations of longitudinal changes in blood biomarkers of dementia with the proportion of genetically inferred African ancestry. Neurology. (2025) Sun Y, Xu H, Ye K. Genome-wide association studies and multi-omics integrative analysis reveal novel loci and their molecular mechanisms for circulating polyunsaturated, monounsaturated, and saturated fatty acids. Human Genetics and Genomics Advances. (2025) Ihejirika SA, Chiang AH#, Singh A#, Stephen E#, Chen H, Ye K. A multi-level gene-diet interaction analysis of fish oil supplementation and 14 circulating polyunsaturated fatty acids-related traits identifies the FADS and GPR12 loci. Human Genetics and Genomics Advances. (2025) Zhang Y, Sun Y, Song S, Khankari NK, Brenna JT, Shen Y^, Ye K^. Associations of plasma omega-6 and omega-3 fatty acids with overall and 19 site-specific cancers: a population-based cohort study in UK Biobank. International Journal of Cancer. (2024) Yang S, Cai H, Ye K. Phenome-wide association study of population-differentiating genetic variants around gene ACSL1. Evolution, Medicine, and Public Health. (2024) Sun Y, McDonald T#, Baur A#, Xu H, Bateman NB#, Shen Y, Li C, Ye K. Fish oil supplementation modifies the associations between genetically predicted and observed levels of blood lipids: a cross-sectional gene-diet interaction study in UK Biobank. The American Journal of Clinical Nutrition. (2024) Francis M, Westerman KE, Manning AK, Ye K. Gene-vegetarianism interactions in calcium, estimated glomerular filtration rate, and testosterone identified in genome-wide analysis across 30 biomarkers. PLOS Genetics. (2024) Zhang Y, Sun Y, Yu Q, Song S, Brenna JT, Shen Y^, Ye K^. Higher ratio of plasma omega-6/omega-3 fatty acids is associated with greater risk of all-cause, cancer, and cardiovascular mortality: A population-based cohort study in UK Biobank. eLife. (2024) Ge A*$, Sun Y*, Kiker T$, Zhou Y, Ye K. A metabolome-wide Mendelian randomization study prioritizes potential causal circulating metabolites for multiple sclerosis. Journal of Neuroimmunology. (2023) Sun Y, Chatterjee R#, Ronanki A#, Ye K. Circulating polyunsaturated fatty acids and COVID-19: a prospective cohort study and Mendelian randomization analysis. Frontiers in Medicine. (2022) Yang S, Ye K. Recent advances in understanding the adaptive evolution of metabolic genes and traits. Current Opinion in Clinical Nutrition and Metabolic Care. (2021) Francis M, Li C, Sun Y, Zhou J, Li X, Brenna JT, Ye K. Genome-wide association study of fish oil supplementation on lipid traits in 81,246 individuals reveals new gene-diet interaction loci. PLOS Genetics. (2021) Ye K, Gao F, Wang D, Bar-Yosef O, Keinan A. Dietary adaptation of FADS genes in Europe varied across time and geography. Nature Ecology and Evolution (2017)Kothapalli KSD*, Ye K*, Gadgil MS, et al. Positive selection on a regulatory insertion–deletion polymorphism in FADS2 influences apparent endogenous synthesis of arachidonic acid. Molecular Biology and Evolution (2016).Ye K*, Cao C*, Lin X, O'Brien KO, Gu Z. Natural selection on HFE in Asian populations contributes to enhanced non-heme iron absorption. BMC Genetics (2015).Ye K^, Lu J, Ma F, Keinan A, Gu Z^. Extensive pathogenicity of mitochondrial heteroplasmy in healthy human individuals. Proceedings of the National Academy of Sciences (2014).Ye K^, Lu J, Raj SM, Gu Z^. Human expression QTLs are enriched in signals of environmental adaptation. Genome Biology and Evolution (2013).Ye K & Gu Z. Recent advances in understanding the role of nutrition in human genome evolution. Advances in Nutrition (2011).
