Research Experience

Westlake University, School of Life Sciences Hangzhou, China

Visiting Student, Advisor: Prof. Jian Yang March 2024 – June 2024

• Participated in a groundbreaking project combining spatial transcriptomics with genetics, utilizing an unprecedented dataset encompassing nearly all publicly available spatial transcriptomics data to date. Contributed to comprehensive analysis starting from raw FASTQ sequences, ensuring uniform processing across all datasets.

• Assisted in developing and implementing advanced methodologies to identify cell type-specific eQTLs, leveraging the extensive expression data from various cell types to call SNPs and uncover nuanced genetic regulatory mechanisms at a cellular level.

• This innovative approach, integrating cutting-edge spatial transcriptomics technology with advanced genetic analysis methods, set a new standard in the field, providing unparalleled insights into spatial gene regulation and cell-type-specific genetic effects.

Mayo Clinic, Department of Quantitative Health Sciences Rochester, MN

Research Assistant, Advisor: Prof. Jun Chen March 2023 – March 2024

• Collaborated on the development of an R package for longitudinal microbiome and multi-omics data analysis, contributing over 12,000 lines of R code and authoring more than 10,000 words for the project's wiki. This package will be integrated into the MicrobiomeStat package.
• Created MicrobiomeGallery, a shiny platform for sharing advanced microbiome visualizations and code in an open-source, reproducible environment. Connect with fellow researchers, exchange knowledge, and contribute to the ever-growing microbiome community.

Case Western Reserve University, School of Medicine Cleveland, OH

Research Assistant, Advisor: Prof. Liangliang(Lyon) Zhang June 2022 – March 2023

• Processed 16S rRNA microbial community data using Qiime2, Galaxy, Phyloseq, and MicrobiomeAnalyst.

• Developed and implemented the ggpicrust2 R package, designed specifically for the analysis and visualization of PICRUSt2-predicted functional profiles in Metagenomics. This package has achieved over 5000 total downloads on both CRAN and Github and has been widely used by researchers in the field.

• Summarized the applications of statistical methods and machine learning techniques on microbiome research (writing a review for submission).

Southern Medical University & University of North Carolina at Chapel Hill, Institute for Global Health

Research Assistant, Advisor: Prof. Dong(Roman) Xu March 2021 – August 2022

• Assisted pediatricians in the development of standardized patient scenarios for evaluating the quality of basic medical care in China, specifically focused on pediatric diarrheal disease.

Skills

Technical Skills: R, Python, C, SAS, SPSS, Qiime2, Galaxy, MicrobiomeAnalyst

Education

Texas A&M University College Station, TX Ph.D. in Statistics, Advisors: Prof. Jun Chen and Prof. Xianyang Zhang August 2024 – May 2029 (Expected)

Publications

Chen Yang, Jiahao Mai, Xuan Cao, Fabio Cominelli, Aaron Burberry, Liangliang(Lyon) Zhang (2023). ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization. Bioinformatics. DOI: https://doi.org/10.1093/bioinformatics/btad470

Chen Yang, Jun Chen (2023). MicrobiomeStat: A Comprehensive R Package for Longitudinal Microbiome and Multi-Omics Data Analysis. Planned to submit to Bioinformatics.