Jin Seok (Andy) Lee
Cancer Immunogenomics / Bioinformatics
Bio
I am a bioinformatics and computational biology PhD student in the Personalized Immunotherapy Research Lab at the University of North Carolina at Chapel Hill, where I am co-advised by Dr. Alex Rubinsteyn and Dr. Benjamin Vincent. My thesis focuses on developing computational methods for accurate identification of neoantigens using long-read DNA and RNA sequencing data from tumors for development of personalized immunotherapies. Previously, I worked as a bioinformatics researcher at the National Cancer Center Korea, where I developed computational approaches for analyzing mutational signatures operative in tumor genomes.
Key Research Interests
I am keenly interested in developing state-of-the-art software programs that enable personalized immunotherapy development.
- Neoantigen discovery
- Variation graph based approaches for construction of personalized genome, transcriptome, and proteome.
- Methods for accurate alignment, variant calling, haplotype phasing, and assembly of long reads.
- Computational approaches for immunogenic neoantigen selection and validation.
- Tumor heterogeneity and evolution
- Decomposition and reconstruction of mutational signatures.
- Clonality analysis (bulk and single cell).
- Chromatin organization for structural variant identification.
- Benchmarking
- Simluation of ground truth for baseline establishment.
- Scalable pipeline development.
- Comparative analysis of software programs for performance and accuracy evaluation.
Selected Papers
Co-first author (*)
ACE configurator for ELISpot: optimizing combinatorial design of pooled ELISpot assays with an epitope similarity model. Jin Seok Lee*, Dhuvarakesh Karthikeyan, Misha Fini, Benjamin G. Vincent, Alex Rubinsteyn. Briefings in Bioinformatics. 2024. doi: 10.1093/bib/bbad495.
Deciphering the evolutionary history of complex rearrangements in head and neck cancer patients using multi-Omic approach. Jeesoo Chae, Jin Seok Lee*, Jongkeun Park, Dong-Sung Lee, Weon Seo Park, Benjamin Clock, Jesse R. Dixon, Yuh-Seog Jung, Dongwan Hong. bioRxiv. 2022. doi: 10.1101/2022.08.19.504509
FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures. Hyunbin Kim, Andy Jinseok Lee*, Jongkeun Lee, Hyonho Chun, Young Seok Ju, Dongwan Hong. Genome Medicine. 2019. doi: 10.1186/s13073-019-0695-x
Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures. Jongkeun Lee, Andy Jinseok Lee*, June-Koo Lee, Jongkeun Park, Youngoh Kwon, Seongyeol Park, Hyonho Chun, Young Seok Ju, Dongwan Hong. Nucleic Acids Research. 2018. doi: 10.1093/nar/gky406
See more here.
Personal Life
I was born in Korea and spent my formative years in Indonesia and Singapore. Now that I live in North Carolina, in the South, I guess you could say I’m a South Korean. I also spent years in Michigan, enduring the polar vortex winters. From sweating through Southeast Asia to shivering in the Midwest, I’ve basically covered the entire weather spectrum - and lived to tell the tale.
In my free time, I channel my inner dramaturg as a theater enthusiast (big fan of PlayMakers), play mad scientist in the kitchen (results vary), and stay active with golf, tennis, and pickleball - because longevity pairs well with racquets.