Sung Rye Park

COMPUTATIONAL BIOLOGIST
Specializing in Translational Drug Discovery

Computational Biologist with 7+ years delivering multi-omics integration and translational biomarker analyses in pharma collaborations (BMS, Takeda, Japan Tobacco)

Builds analytical frameworks that bridge biology, machine learning, and multi-omics data — designing systems-level approaches that make sense of heterogeneous biological datasets.

Domains: Immuno-oncology · Metabolic disease (NAFLD) · Neurodegeneration (AD, TBI)
Expertise: Single cell · Multi-omics integration · Machine Learning · Pipeline development · Analytical templates · Interactive reports


CV   GitHub   LinkedIn

Featured Projects

Novel function of Tle3: Multi-omics approach

  • Four modalities with pair-wise integration
  • scRNA-seq, RNA-seq, ATAC-seq, Cut&Run (TLE3)
  • Nature Immunology (2024); co-first author

    Pair-wise integration Immunology T cell Lineage

STING Agonist Response: BMS Collaboration

  • Responding cell type stratification
  • scRNA-seq + scTCR-seq
  • Cell Reports Medicine (2024)

    Single-cell RNA-seq scTCR-seq Immunology Oncology Deconvolution

Virtual Patient Cohort Generation (MicroIRAD)

  • CVAE framework learning TCGA-LUAD
  • 400+ synthetic patients
  • Patient-Model cell line pair similarity score (10,000+)
  • Preclinical go/no-go decision support

    Deep Learning PyTorch/Tensorflow CVAE TCGA LUAD AutoEncoder

Cell image + RNA-seq by MOFA2

  • Phenotypic profiling + Transcriptome
  • Large scale compound response study
  • End-to-end integration pipeline

    MOFA2 Cell Painting Transcriptome Drug response Human lung cancer Multiomics

Selected Publications

Nature Immunology 2024
The transcriptional cofactor Tle3 reciprocally controls effector and central memory CD8+ T cell fates.
Co-first author  ·  View Paper →
Cell Reports Medicine 2025
Immune targeting of triple-negative breast cancer through a clinically actionable STING agonist-CAR T cell platform.
View Paper →
Cell 2021
Seq-Scope: Microscopic examination of spatial transcriptome.
View Paper →
Cell Reports 2021
Single cell transcriptome analysis of colon cancer cell response to 5-fluorouracil-induced DNA damage.
First author  ·  View Paper →
AJP-Endocrinology and Metabolism 2020
Holistic Characterization of Single Hepatocyte Transcriptome Responses to High Fat Diet.
First author  ·  View Paper →

Analysis Workflows

Single Cell RNA-seq
QC, integration (Harmony), UMAP/clustering, cell type annotation, trajectory, AUC, scTCR-seq preprocessing
View Workflow →
Bulk RNA-seq
PCA, TPM, DEG analysis, GSEA/ssGSEA, K-means clustering, feature selection
View Workflow →
NK cell identification using ML
Elastic Net for feature selection, K-means + DEG-based pattern identification (bulk RNA-seq)
View Example →
Chromatin & Epigenomics
ChIP-seq, ATAC-seq, CUT&RUN pipelines — peak calling, motif analysis
View Workflow →
Omics Analytical Pipelines
Pipelines Collections; scRNAseq, RNA-seq, DNA-seq, ML
View Workflow →

Experience

  • Battelle (2025-Present) : Data Scientist II, Bioinformatics
  • Dana Farber Cancer Institute (2022-2024) : Senior Bioinformatics Scientist
  • Hackensack Meridian Health (2021-2022) : Postdoctral fellow
  • University of Michigan (2017-2020) : Postdoctral fellow

GitHub Repositories

Repository Description
tle3-multiomics-NI2024 Multi-omics analysis for the TLE3 study (Nature Immunology, 2024), integrating RNA-seq, ATAC-seq, and ChIP-seq.
pubmed-local-rag Local RAG pipeline for querying PubMed literature using LLMs — offline, context-aware search without API calls.
lung-tme-deconv-profiler Bulk RNA-seq deconvolution pipeline for tumor microenvironment (TME) profiling in lung cancer.
rnaseq_local_chat Local LLM chat interface for interactive RNA-seq exploration — query DEG and pathway results in natural language.