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
- scRNA-seq pipeline
- RNA-seq pipeline
- ChIP-seq/Cut&Run/ATAC-seq pipeline
- Machine Learning application
- Public DB
Public Pages
Github LinkedIn
Skills
- Proficient in a wide array of NGS data pipelines and bioinformatics
analyses including scRNA-seq, scTCR-seq, CITE-Seq, ATAC-seq, bulk
RNA-seq, as well as integrative approaches with TCGA and CCLE for
genomic and epigenomic studies
- Proficient in Linux, with programming skills in Python and R, and
skilled use of bioinformatics tools including Cellranger, Salmon, and a
suite of sequence alignment and analysis utilities
- Well-versed in peak calling, genomic visualization, and analysis
using open- source platforms such as Seurat, scanpy, and the USCC Genome
Browser
- Expertise in pathway and network analysis to elucidate complex
biological pathways, and statistical analysis for robust genomic data
interpretation
- Familiarity with high-performance computing environments and adept
at managing in-lab NGS pipelines, ensuring quality and
reproducibility
- Skilled in data visualization and presentation, utilizing tools like
ggplot2, Shiny, and Rmarkdown, to effectively communicate complex data
to diverse audiences
- Expertise in immunology, oncology, and molecular biology with
practical experience in public dataset analysis
- Developed and maintained specialized assay platforms including
Drop-seq, Seq-well, and Seq-scope
- Proficient in NGS library generation, particularly with single cell
10X genomics and RNA-seq
- Autonomous work style, efficiently conducting research with minimal
oversight Guiding and mentoring interns in bioinformatics practices and
project work
- Consulting with collaborators to identify and apply novel
bioinformatics analysis methods
- Managing documentation and workflow sharing across collaborative
platforms
- Keeping meticulous records of both raw and processed data
storage
Experience
Senior Bioinformatics scientist at Dana Farber Cancer Institute
2022-
- TCGA-BRCA data analysis (MSLN+TROP2)
- DS-1062a Testing data analysis (scRNA-seq + RNA-seq)
- PDX model based Oncogenic driver pattern study (RNA-seq)
- DGK inhibitor efficacy testing in combination with Nivolumab for
SCLC
- DS-1062 and Pembrolizumab testing for SCLC
- EZH2 inhibitor candidates searching using ChIP-seq
- Evaluation of STING agonist (ADU-100) effects in mouse PBMCs and the
tumor immune environment
- TAK-676 and PD-1 blockade in SCLC
- Immune cell trafficking within in-house device culture
- Integrative analysis of anti-CD47 therapy efficacy in PTCL-resistant
mouse models
- Supporting manuscript writings.
- (more)
Postdoctoral Fellow at Hackensack Meridian Health
- Reprogramming fate of central memory CD8+T targeting transcriptional
co-factor Tle3 (Nature Immunology, 2024)
- Comparison of chronic infection and protein immunization in the
development of CD4+ Tfh cells regulated by costimulatory molecules
Icos
- CITE-seq, custom pipeline development and applications
Postdoctoral Fellow at University of Michigan
- Various NGS platform in-lab setting (DROP-seq, Seq-well, BD-Rapsody,
and Seq-scope (Contribution to the platform development, Cell,
2021)
- Single cell transcriptome study of colon cancer cell response to
5FU-induced DNA damage (Cell Reports, 2020)
- Holistic characterization of single Hepatocyte transcriptome
responses to high fat diet (American Journal of Physiology, 2020)
- Supporting role: flow-cytometry, immunoblotting, qPCR, mouse
surgery, etc
Publications
- The transcriptional cofactor Tle3 reciprocally controls effector and
central memory CD8+ T cell fates. (Nature Immunology, 2024. X.Zhao,
W.Hu, S.R.Park, S.Zhu, S.S.Hu, C.Zang, W.Peng, Q.Shan ,H.H. Xue.
co-first (Zhao, W.Hu, Park and Zhu as co-first authors
with equal contribution) (https://doi.org/10.1038/s41590-023-01720-w)
- SiftCell: A robust framework to detect and isolate cell-containing
droplets from single-cell RNA sequence reads. (Cell Systems, 2023)
Jingyue Xi, Sung Rye Park, Jun Hee Lee and Hyun Min Kang. (https://doi.org/10.1016/j.cels.2023.06.002)
- Sublethal whole-body irradiation induces permanent loss and
dysfunction in pathgen-specific circulating memory CD8T cell
populations. (PNAS, July 2023) Mohammad Heidarian, Iassac J Jensen,
Shravan Kumar Kannan, Lecia L Pewe, Mariah Hassert, Sung Rye Park,
Hai-Hui Xue, John Harty, Vladimir Badovinac. (https://doi.org/10.1073/pnas.2302785120.)
- Simultaneous loss of TSC1 and DEPDC5 in skeletal and cardiac muscles
produces early-onset myopathy and cardiac dysfunction associated with
oxidative damage and SQSTM1/p62 accumulation. (Autophagy, 2021)
Chun-Seok Cho, Yongsung Kim, Sung-Rye Park, Boyoung Kim, Carol Davis,
Irene Hwang, Susan V Brooks, Jun Hee Lee, Myungjin Kim. (https://doi.org/10.1080/15548627.2021.2016255)
- Seq-Scope: Microscopic examination of spatial transcriptome using
Seq-Scope. (Cell, 2021) Chun-Seok Cho, Jingyue Xi, Yichen Si, Sung-Rye
Park, Jer-En Hsu, Myungjin Kim, Goo Jun, Hyun-Min Kang, Jun Hee Lee. (https://doi.org/10.1016/j.cell.2021.05.010)
- Single cell transcriptome analysis of colon cancer cell response to
5-fluorouracil-induced DNA damage (Cell Reports, 2020) Sung Rye Park,
Sim Namkoong, Zac Zezhi Zhang, Leon Friesen, Euisik Yoon, Chang H. Kim,
Hojoong Kwak, Hyun Min Kang and Jun Hee Lee. (https://doi.org/10.1016/j.celrep.2020.108077)
first
- Holistic Characterization of Single Hepatocyte Transcriptome
Responses to High Fat Diet (American Journal of Physiology-Endocrionlogy
and Metabolism, 2020) Sung Rye Park, Chun-Seok Cho, Hyun Min Kang and
Jun Hee Lee. (https://doi.org/10.1152/ajpendo.00391.2020)
first
- Concurrent activation of growth factor and nutrient arms of mTORC1
induces oxidative liver injury. Cell Discovery volume 5, Article number:
60 (2019) Chun-Seok Cho, Allison Ho, Sim Namkoong, Sung-Rye Park,
Shuangcheng Wu, Boyoung Kim, Amanda James, Bondong Gu, Ian A. Semple,
Mohamed A. Tohamy, Sumeet Solanki, Uhn-Soo Cho, Joel K. Greenson, Yatrik
Shah, Myungjin Kim, Jun Hee Lee. (https://doi.org/10.1152/ajpendo.00391.2020)
Education
- Ph.D. Plant Biology, University of Texas at Austin 2017
- MA. Biology Seoul National University 2010
Last update: 2024-09-28