Yiran Zhao

Research Experience

Ph.D. Research Projects

• Sleep & Diet on Immunity & Chronic Health – Multi-omics exposure-immune association study (Accepted)
Description: Exposures that disrupt the immune system can impact human health. This study aimed to understand immune variability influenced by exposures from a systems biology and multi-omics perspective. We recruited 1,001 healthy participants and collected 183 exposure, 1,332 immunophenotypes, whole blood transcriptome and plasma metabolome. Through exposure-immune wide association analysis, we identified 81 significant signals, with sleep and diet emerging as dominant exposures affecting the immunome (immune cells and function). Notably, compared with short-term late sleep onset, long-term late sleep onset triggered chronic inflammation with inducing metabolic changes. Besides, diet-related exposures mainly influence immune cell functions. We further quantified the mediation effects of exposures, omics and immunophenotypes, and further demonstrated that these effects reflect human immune health or chronic diseases. Our study offers comprehensive views of immunome variation affected by exposures and omics, and hold promise for guidance for future health assessment and management.
Figure: Graphical abstract
• Gut Microbiota & Metabolites in Insulin Resistance – Mediation analysis of dietary inflammatory score (In Preparation)
Description: It is known that Dietary Inflammatory Score (DIS) have an impact on insulin resistance. However, how DIS affect insulin resistance through plasma metabolites and gut microbiota remains unknown. This study analyzed the relationship among DIS, insulin resistance and plasma metabolites or gut microbiota; and verified that altering gut microbiota can replace some of the health effects brought about by dietary pattern changes.
Figure: Graphical abstract

• Immunophenotypic Profiling of BMI/WHR – Health heterogeneity & lifestyle influences
• Frailty Stratification via Immune Features – Subtyping & immune frailty index
• Seasonal Protein Patterns & Disease – UK Biobank analysis

Undergraduate Project

• Stemness monitoring of mesenchymal stem cells via qRT-PCR & morphological analysis
Description: Human umbilical cord-derived mesenchymal stem cells (hUCMSCs) are promising therapeutic agents, but their industrial-scale manufacturing requires scalable quality control methods. To overcome the inefficiency of traditional stemness assays, this project developed and validated a rapid qRT-PCR method for monitoring stemness-related genes across passages. This approach was complemented by quantitative morphological and metabolic analyses, establishing an efficient framework for future large-scale production.

Research Skills

• Bioinformatics: R, Python, Shell, Linux, HPC, Multi-omics, Single-cell, GWAS, Machine Learning
• Wet Lab: Flow cytometry, PCR/qPCR, Stem cell culture, Sequencing library prep, Protein expression&purification

Publications

First Author

• Zhao, Yiran* et al. “The Influence of Sleep and Diet on Human Peripheral Immunity and Chronic Health Conditions.” Research (2025): n. pag.
• Zhao Y* et al. "The gut microbiome and plasma metabolites modulates the association between a inflammatory diet and insulin resistance" (In Prep)
• Zhou S, Zhao Y* et al. "Immunophenotypic profiling of obesity characterizes health heterogeneity and lifestyle influences" (In Prep)

Co-authored

• Li W, Li K, Zhou P, Cheng Y, Zhao Y*, Meng X, Niu Y, Zong G, Kan H, Wang S. Proteomic mediation of air pollution and diseases: A comprehensive analysis in the UK Biobank cohort. Nature Communications (2025)
• Gao J, Luo Y, Li H, Zhao Y*, Zhao J, Han X, Han J, Lin H, Qian F. Deep Immunophenotyping of Human Whole Blood by Standardized Multi-parametric Flow Cytometry Analyses. Phenomics. 2023 Feb 23;3(3):309-328. doi: 10.1007/s43657-022-00092-9.
• Han J, Gao J, Ma Y, Li Y, Wu C, Le S, Zhao Y*, Li H, Luo Y, Han X, Guo Y, Li Y, Zhou G, Jin L, Wang J, Qian F. Distinct immune cell profiles associated with high-altitude hypoxia and severe acute mountain sickness. The Journal of Physiology. 2025 Aug 6. doi: 10.1113/JP288584.
• Zhao J, Han X, Li H, Luo Y, Fang Y, Wang Y, Gao J, Zhao Y*, Han J, Qian F. Analysis of the Immune Response by Standardized Whole-Blood Stimulation with Metabolism Modulation. Phenomics. 2023 Sep 12;4(1):81-89. doi: 10.1007/s43657-023-00114-0.
• Luo Y, Gao J, Su X, Li H, Li Y, Qi W, Han X, Han J, Zhao Y*, Zhang A, Zheng Y, Qian F, He H. Unraveling the immunological landscape and gut microbiome in sepsis: a comprehensive approach to diagnosis and prognosis. EBioMedicine. 2025 Mar;113:105586. doi: 10.1016/j.ebiom.2025.105586.
• Li Z, Ning X, Zhao Y*, Zhang X, Xiao C, Li Z. Efficient One-Pot Synthesis of Cytidine 5'-Monophosphate Using an Extremophilic Enzyme Cascade System. J Agric Food Chem. 2020 Aug 26;68(34):9188-9194. doi: 10.1021/acs.jafc.0c04055.

Patent

CN2025104699649 – "Method and device for Constructing a machine Learning model for lifestyle-related Immune Scoring" (Feng Qian, Sijia Wang, Yiran Zhao*, Wenran Li, Bingjie Li, Jian Gao)

Conferences & Awards

• Oral Presentation - The Announcement of The 4th National Conference on Systems Biology (2025)
• Outstanding Academic Presentation – "Human Biology" academic exchange activities (2025)
• Outstanding Poster – Life Science Forum of Fudan University Doctoral Academic Forum (2024)
• Outstanding Student – Fudan University (2022)
• Outstanding Graduate & Thesis – ECUST (2021)
• iGEM (International Genetically Engineered Machine Competition) Silver Award (2021)
• Mathematics Competition Third Prize – ECUST (2018)

Professional Activities

• Publishing Editor (Part-time) – Phenomics Journal:

Assisting the editorial office in manuscript processing (invite reviewers, format proofreading)

Operating the publicity platforms and making the publicity products of Phenomics

Assisting in the organization of journal meetings, domestic and international conference affairs and expert reception

• Participate in the construction of the cohort:

Cohort Data Collection & Immunome Data Processing

Flow Cytometry Gating & QC Pipeline Design