Professional summary


Experienced Senior Bioinformatics Scientist with a strong background in computational biology, specializing in the innovative application of immunotherapy in oncology. Expert in analyzing and visualizing complex NGS data from oncology clinical trials, leveraging advanced ML algorithms to extract patient-specific features for further analysis. Proficient in integrating diverse sequencing assays, such as TCR sequencing, scRNA-seq, and bulk RNA seq, along with public resources, to identify critical biomarkers and therapeutic targets. My collaborative efforts across multidisciplinary teams have significantly advanced project outcomes and contributed to impactful publications using integrative approaches from transcriptomics and epigenomics to reveal novel insights into cancer biology.

Sung Rye Park’s resume (pdf)


Works

General Workflow Overview

  1. scRNA-seq pipeline
  2. RNA-seq pipeline
  3. ChIP-seq/Cut&Run/ATAC-seq pipeline
  4. Machine Learning application
  5. Public DB



Single Cell RNA-seq workflow

General Single cell RNA-seq workflow




RNA-seq Analysis using TCGA DB data

TCGA-BRCA Transcriptome Analysis

  • PCA
  • DEG Anaysis
  • GSEA (HALLMARK)
  • ssGSEA





Miscellaneous

Data_Processing in Linux env
WDL example
BCR-seq info (Antibody_discovery_Platform)
Simple shiny app
Basic Github usage
cellranger docker setup
MAF analysis

Learning new methods

CRISPR Screening method comparison (Korean/English)



Conference/Seminar Note

2024

   Conference Summary Report: 10X Genomics User Group Meeting 2024
   Conference Note (personal): 2024 Festival in Genomics in Boston






Project Tracking Example



(works/index)




Public Pages

Github
LinkedIn

First/co-first authorship publications (pdf)

The transcriptional cofactor Tle3 reciprocally controls effector and central memory CD8+ T cell fates. (Nature Immunology, 2024)

Single cell transcriptome analysis of colon cancer cell response to 5-fluorouracil-induced DNA damage (Cell Reports, 2020)

Holistic Characterization of Single Hepatocyte Transcriptome Responses to High Fat Diet (American Journal of Physiology-Endocrionlogy and Metabolism, 2020)



Skills



Experience


Publications

Education



Last update: 2024-09-28