Xin Dong

Xin Dong

PhD in Bioinformatics.

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 EXPERIENCES

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. With the advances of single-cell multiomics techniques, we updated it to SCRIPro, which suits both single-cell and spatial multiomics data.
    • Developed TISCH (Tumor Immune Single Cell Hub) and TISCH2, a curated resource integrating single-cell transcriptome profiles from ~6 million cells across 50 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.
    • We developed and maintained the Cistrome Data Browser, which hosts many public cistrome sequence datasets, offering a user-friendly interface to access the data quality and the results of downstream analysis.

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/spatial RNA/ATAC-seq analysis; Epigenome data analysis (ChIP-seq, ATAC-seq, etc.); Machine learning (PyTorch, scikit-learn)
  • Programming: Python; R; Shell; JavaScript; MySQL
  • Tools & Frameworks: Git; Django; Vue.js; Bootstrap
  • Cloud & HPC: Snakemake; AWS/GCP computation
  • Server operation and maintenance: Ubuntu; CentOS / Rocky Linux

CONFERENCES

  • 2024
    • Poster Speaking, Human Cell Atlas Asia 2024, Hong Kong SAR, China
    • 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 (10 of the University), 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 & 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