Methods and tools

Research interests, technical skills, and the tools behind them.

Analysis pipelines are published on GitHub at github.com/Sejung98.

Research interests

Investigating tumor evolutionary dynamics, structural variations, and multi-omics prognostication through rigorous computational genomics and functional biology.

Tumor Evolution & Clonal Architecture

Reconstructing intra-tumor heterogeneity, subclonal phylogenies, and temporal ordering of somatic events using high-depth whole-genome sequencing (WGS).

WGS Tumor Phylogeny Clonal Dynamics Temporal Ordering

Structural Variation & Long-Read Genomics

Characterizing complex genomic rearrangements, whole-genome doubling (WGD), and cryptic structural alterations using Oxford Nanopore and PacBio long-read platforms.

Long-Read SV Nanopore / PacBio WGD Chromosomal Instability

Multi-Omics Prognostication & Survival Modeling

Building predictive clinical risk models and prioritizing therapeutic biomarkers by integrating multi-omics profiles (genomics, transcriptomics, epigenomics) in breast and ovarian cancers.

Survival Analysis Risk Modeling Multi-Omics Integration Biomarker Discovery

Translational Cancer Systems Biology

Bridging high-throughput in silico pipelines with wet-lab experimental validation and patient cohorts to identify actionable clinical vulnerabilities.

Functional Validation Precision Oncology Early-Onset Cancers Systems Biology

Technical skills

Integrated stack spanning computational bioinformatics, statistical modeling, and pipeline engineering.

Genomics & Bioinformatics

Next-generation & long-read sequencing

End-to-end processing of WGS, WES, RNA-seq, and long-read datasets (Oxford Nanopore, PacBio). Personally configured and established the Hartwig Medical Foundation (HMF) whole-genome pipeline in our laboratory, actively running comprehensive tumor genomic analyses using Nextflow.

WGS / WES Long-Read SV RNA-seq CNA & WGD Hartwig (HMF) Pipeline Nextflow GATK / Mutect2 Sniffles

Evolution & Phylogeny

Subclonal architecture & timing

Clonal deconvolution, subclonal clustering (PyClone, SciClone), tumor phylogenetic tree reconstruction (PhylogicNDT), and temporal ordering of driver events.

Clonal Deconvolution PyClone Phylogenetic Trees Temporal Ordering Subclonal Kinetics

Statistical Modeling & ML

Multi-omics & survival prediction

Cox proportional hazards, Kaplan-Meier estimation, regularized regression (Lasso/ElasticNet), multi-omics integrative clustering, and robust clinical biomarker prioritization.

Survival Analysis Cox-PH Multi-Omics Integration Biomarker Scoring scikit-learn

Programming & Pipelines

Reproducible code & HPC

Scalable pipeline execution on Linux / HPC clusters (SLURM). Python & R data science ecosystems, Git / GitHub version control, and containerized workflows with Nextflow & Docker.

Python R / Bioconductor Bash / Linux SLURM / HPC Git & GitHub Nextflow

Wet Lab & Experimental Assays Undergraduate research experience

In vitro & in vivo molecular validation

Mammalian cell culture, flow cytometry (FACS), Western blotting, ELISA, cytokine multiplex assays, and murine disease models for validating in silico predictions.

Cell Culture FACS Western Blot ELISA Cytokine Assays Murine Models