Mapping how tumors evolve — one genome at a time.
We study extrachromosomal DNA, tumor evolution and intratumoral heterogeneity through large-scale computational and statistical analysis of cancer genomes.
Recent News
"Extrachromosomal DNA in cancer: mechanics, functions, and therapeutic implications"
A new review by Boyoon Kim, published in Signal Transduction and Targeted Therapy, exploring the mechanics, functions, and therapeutic implications of ecDNA.
Single-cell resolution tracking of oncogenic ecDNA inheritance
Co-authored by Eunchae, published in Experimental & Molecular Medicine — novel insight into ecDNA dynamics via single-cell analysis.
Boyoon Kim wins the Grand Prize at SKKU Research Matters Plus
Honored with the Grand Prize (대상) at the 1st Graduate Research Achievement Competition+ for her outstanding research contribution.
Hyunjeong awarded the KOSAF Doctoral Excellence Scholarship
Selected for the Doctoral Excellence Scholarship in Science and Engineering from the Korea Student Aid Foundation.
Boyoon Kim presents at AACR 2026 — a lab milestone
Our first lab member to present at the AACR Annual Meeting, San Diego, drawing strong interest from academia and industry.
Boyoon Kim receives the KOBRA Travel Award
The Global-TA award supported her participation and presentation at AACR 2026.
Tailorable porous collagen hydrogels for ecDNA research
Co-first authored by Jiwon Shon, published in Theranostics — a 3D hydrogel platform that preserves ecDNA structures.
ecDNA foundation model proposal selected by NVIDIA
Selected for the NVIDIA Academic Grant Program with Prof. Se-Young Chun (SNU) — 32,000 A100 GPU-hours awarded.
IDH-mutant gliomas arise from glial progenitor cells
Published in Science — identifying glial progenitor cells as the cell of origin in IDH-mutant gliomas.
Yoonjoo awarded a National Research Foundation doctoral research grant
Funds her PhD research into how ecDNA interacts with micronuclei as tumors acquire chemotherapy resistance.
Jueon awarded a National Research Foundation master's research grant
Supports her single-cell multi-omics study of ecDNA in glioblastoma.
Prof. Kim invited to present at ICBTRT 2025, Japan
Presented our longitudinal characterization of ecDNA amplifications in adult glioma at the 24th International Conference on Brain Tumor Research and Therapy.
Team
Fifteen of us, working across bioinformatics, wet-lab biology, and computation. Click any name to visit their profile.
- Hoon Kim, PhDPrincipal Investigator
- Sanghyun Kim, PhDResearch Professor
- Heesuk Chung, BS·BAResearch Assistant
- Seunghyun Kang, BSResearch Assistant
- Yoonjoo Nam, BSResearch Assistant
- Eunchae Yeo, BSResearch Assistant
- Hyunjeong Sun, MSResearch Assistant
- Jiwon Shon, BSResearch Assistant
- Junghyun Kim, BSResearch Assistant
- Boyoon Kim, BSResearch Assistant
- Jaeho Jang, MSResearch Assistant
- Hyeongjin Cho, Pharm.D.Research Assistant
- Jueon Kim, BSResearch Assistant
- Jongkyu Jang, Pharm.D.M.S. Candidate
- Hyesoo KimUndergraduate Intern
Research
“Our lab is all about big data.”
A major cause of cancer treatment failure is the development of therapy resistance in tumors, which evolve by accumulating tumor-promoting mutations and modified chromosome structures. Our lab addresses this through computational and statistical analysis of large-scale biomolecular data — centered on extrachromosomal DNA (ecDNA), work spanning long- and short-read sequencing, single-cell and spatial multiomics, FISH validation, and structural variant analysis, alongside collaborators across cancer biology, epigenetics, structural biology, bioimaging, and tumor microenvironment research.
ecDNA: Mechanics, Functions & Therapeutic Implications
Our most comprehensive synthesis to date on ecDNA's mechanical properties, biological functions, and therapeutic angles — building on our pan-cancer survey finding circular ecDNA in over 25 of 29 cancer types and our latest single-cell tracking of ecDNA inheritance.
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Tumor Evolution & Glioma Origin
From non-chromosomal ecDNA amplification driving intratumor heterogeneity to tracing IDH-mutant glioma back to the glial progenitor cells that first carry the driver mutation — with the GLASS consortium we co-founded.
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ecDNA Across Cancer Types & New Research Platforms
Mapping ecDNA in gastric and breast cancer and Barrett's esophagus, and building tailorable 3D collagen hydrogel platforms that better preserve ecDNA structures for long-term study.
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Computational Tools for Amplicon & SV Analysis
We co-developed AmpliconSuite, an end-to-end workflow now used broadly across the field for detecting and reconstructing focal amplifications — including ecDNA — from sequencing data.
Read more →Recent Publications
Breast cancer subtypes follow very different paths after chemotherapy given before surgery, leaving behind distinct patterns of residual disease — a step toward subtype-specific follow-up treatment.
The first pan-cancer map of ecDNA amplification, showing these circular DNA structures are far more common than once thought — and that they predict worse outcomes as tumors advance.
Extends ecDNA's reach beyond the cancers we usually study, showing it also drives the earliest steps of Barrett's esophagus turning cancerous.
Also on Google Scholar and ORCID.
Open Positions
Interested in joining us? Reach out with your CV and a line about what draws you to computational cancer genomics — we'd love to hear from you.
Email the labCollaborators & support