CV

PDF Version [CV]

EDUCATION

Sep.2018 – Jul.2024
Ph.D. in Bioinformatics
School of Life Sciences and Technology, Tongji University, China

Sep.2014 – Jun.2018
B.S. in Biotechnology
School of Life Sciences, Shandong Normal University, China

RESEARCH EXPERIENCE

Graduate Student, Tongji University (2018-2024)

• Developed and applied computational methods to analyze single-cell and spatial data
  • Developed SCRIP (Single-Cell Gene Regulation Inference using ChIP-seq), a method integrating scATAC-seq and bulk TR ChIP-seq to infer single-cell TR activity and targets. SCRIP outperformed motif-based approaches in TR binding activity assessment and enabled identification of TR target genes and construction of single-cell GRNs. It was successfully applied to lineage tracing, cell-type clustering, and cell-type-specific GRN inference in various biological systems.
  • Developed TISCH (Tumor Immune Single Cell Hub), a curated resource integrating single-cell transcriptome profiles from ~2 million cells across 27 cancer types, enabling systematic comparison of gene expression and immune system heterogeneity to inform immunotherapy research.
• Large-scale genomic data mining and integration analysis
  • Developed CHIPS, a pipeline that processes epigenome data into readable results with a single command. CHIPS integrates state-of-the-art tools for cistrome NGS data and automates parameter selection. Built on the Snakemake framework, it is easily deployable on cloud or cluster servers.
    

Undergraduate Student, Shandong Normal University (2014-2018)

• Rapid establishment of H7N9 dominant lineage by intragenic recombination in HA segment
  Undergraduate Dissertation Research

• Screening of newcastle disease virus heat-resistant vaccine by homologous recombination
  Undergraduate Innovation Program (Presided)

• The origin, adaptive evolution and population dynamics of infectious Chicken Anemia Virus in China
  Undergraduate Innovation Program (Involved)

• Diversity of fish in Nansi Lake
  Undergraduate Innovation Program (Involved)

Skills

• Bioinformatics: Single-cell data analysis; High-throughput sequencing analysis; Epigenome data analysis; Machine learning; Deep learning
• Programming: Python; R; Shell; JavaScript; MySQL
• High performance computing: Cloud computing; Cluster computing; Snakemake pipelines; Python package development
• User interface development: Django; Vue.js; Bootstrap
• Code version control system: git
• Server Management: Ubuntu; CentOS / Rocky Linux
• Experiment skills: Cell culture, PCR, Gel electrophoresis

CONFERENCES

• 2024
  • Poster Speaking, The 2nd Yangtze River Delta Bioinformatics Conference, Shanghai, China
• 2023
  • Poster Speaking, Systems Biology of Gene Regulation and Genome Editing, Cold Spring Harbor Conferences Asia, Suzhou, China
  • Poster Speaking, The WLA Research Conference on Cells and Genes, Shanghai, China
  • Poster Speaking, 11st National Conference on Bioinformatics and Systems Biology, Guangzhou, China
• 2021
  • Poster Speaking, Human Cell Atlas Asia 2021 Meeting, Online
  • Poster Speaking, 10th National Conference on Bioinformatics and Systems Biology, Chengdu, China
• 2019
  • Attendance, 14th International Bioinformatics Workshop, Beijing, China

TEACHING

• Teaching assistant, Summer Deep Learning Course, School of Life Sciences and Technology, Tongji University, Shanghai, China, 2023
• Teaching assistant, Summer Bioinformatics Course, School of Life Sciences and Technology, Tongji University, Shanghai, China, 2022
• Teaching assistant, Summer Bioinformatics Course, School of Life Sciences and Technology, Tongji University, Shanghai, China, 2021
• Teaching assistant, Summer Bioinformatics Course, School of Life Sciences and Technology, Tongji University, Shanghai, China, 2020
• Teaching assistant, Dragon Star Course, 14th International Bioinformatics Workshop, Beijing, China, 2019

AWARDS AND DISTINCTIONS

• Outstanding Graduates Awards of Shanghai, Shanghai Municipal Education Commission, 2024
• 17th Academic Pioneer, Tongji University, 2023
• National Scholarship, Ministry of Education of the People’s Republic of China, 2023
• Outstanding Student Leader, Tongji University, 2022
• Outstanding Outstanding Graduate Student Scholarship, Tongji University, 2019
• Outstanding Undergraduate Thesis for Bachelor’s Degree, Shandong Normal University, 2018
• Outstanding Graduates Awards of Shandong Province, Human Resources and Social Security Department of Shandong Province, 2017
• The First Prize of The 15th Challenge Cup Competition in Shandong, Shandong Association for Science and Technology, 2017
• Outstanding Student Leader in Shandong, Shandong Provincial Education Department, 2017
• The Grand Prize of Shandong College Students’ Biochemistry Experiment Skills Competition, Shandong Association of Science & Technology, 2016