Dohoon Lee

220-653

Seoul National University

1 Gwanak-ro, Gwanak-gu

Seoul 08826, Republic of Korea

Hi! I’m Dohoon Lee. I got my Ph.D. from the Interdisciplinary Program in Bioinformatics at the Seoul National University, South Korea, as a member of Bio & Health Informatics Lab advised by professor Sun Kim. Before that I got my bachelor’s degree from the School of Biological Sciences at the Seoul National University, with a minor in Computer Science.

My research interests include computational epigenomics, especially the analysis of DNA methylation patterns within normal and malignant cells. I am deeply curious how the extent of errors in the somatic inheritance of DNA methylation states are systematically controlled. Recently, I am excited to examine the potential of deep learning architectures for the modeling of the complex interactions among chromatin features. I believe such AI-driven approaches will certainly be a new paradigm to pursue unbiased and novel scientific findings in a near future.

Besides, I also care about the reproducibility of research results and reusable analysis procedures. I implement it by modularizing routine analyses as self-contained analysis pipelines with workflow management tools, especially with snakemake!

Here you can see my CV in pdf.

news

Sep 14, 2022	🥈 Ranked 2nd in DREAM Challenge 2022: Predicting gene expression using millions of random promoter sequences
Aug 27, 2021	Got Ph.D. in Bioinformatics at SNU
Jun 27, 2021	Ranked 34st (among ~4000 worldwide) in Bioinformatics Contest 2021. Enjoyed a lot!
Sep 23, 2020	Granted Youlchon AI for All fellowship by Youlchon Foundation, Korea
Sep 26, 2019	🥈 Earned Silver Medal (top 5%) in Kaggle Recursion Cellular Image Classification
Sep 7, 2019	🥈 Earned Silver Medal (top 4%) in Kaggle APTOS 2019 Blindness Detection
Aug 20, 2019	Outstanding paper award from BIOINFO 2019
Jun 21, 2019	Merit award (Bronze prize) from 45th annual meeting of Korean Cancer Association
Feb 24, 2019	Ranked 21st (among 3329 worldwide) in Bioinformatics Contest 2019!
Feb 25, 2018	Ranked 21st (among ~3000 worldwide) in Bioinformatics Contest 2018!

selected publications

AMLs harboring DNMT3A-destabilizing variants show increased intratumor DNA methylation heterogeneity at bivalent chromatin domains

Lee, Dohoon, Koo, Bonil, Kim, Seok-Hyun, Byun, Jamin, Hong, Junshik, Shin, Dong-Yeop, Sun, Choong-Hyun, Song, Ji-Joon, Kim, Jaesung, Jaiswal, Siddhartha, Yoon, Sung-soo, Kim, Sun, and Koh, Youngil

bioRxiv 2023

Bib HTML
@article{lee2023dnmt3a, author = {Lee, Dohoon and Koo, Bonil and Kim, Seok-Hyun and Byun, Jamin and Hong, Junshik and Shin, Dong-Yeop and Sun, Choong-Hyun and Song, Ji-Joon and Kim, Jaesung and Jaiswal, Siddhartha and Yoon, Sung-soo and Kim, Sun and Koh, Youngil}, title = {AMLs harboring DNMT3A-destabilizing variants show increased intratumor DNA methylation heterogeneity at bivalent chromatin domains}, journal = {bioRxiv}, doi = {10.1101/2023.02.13.528223}, publisher = {Cold Spring Harbor Laboratory}, year = {2023}, elocation-id = {2023.02.13.528223}, html = {https://www.biorxiv.org/content/early/2023/02/14/2023.02.13.528223}, bibtex_show = {true}, selected = {true} }

Learning the histone codes with large genomic windows and three-dimensional chromatin interactions using transformer

Lee, Dohoon, Yang, Jeewon, and Kim, Sun

Nature Communications 2022

Bib HTML Code Presentation

@article{lee2022chromoformer,
  author = {Lee, Dohoon and Yang, Jeewon and Kim, Sun},
  title = {Learning the histone codes with large genomic windows and three-dimensional chromatin interactions using transformer},
  journal = {Nature Communications},
  doi = {10.1038/s41467-022-34152-5},
  publisher = {Springer Nature},
  year = {2022},
  code = {https://github.com/dohlee/chromoformer},
  html = {https://www.nature.com/articles/s41467-022-34152-5},
  presentation = {https://youtu.be/PfKabJ7iHJo},
  bibtex_show = {true},
  selected = {true}
}

ISMB2019

PRISM: methylation pattern-based, reference-free inference of subclonal makeup

Lee, Dohoon, Lee, Sangseon, and Kim, Sun

Bioinformatics 2019

Bib HTML PDF Presentation

@article{lee2019prism,
  abbr = {ISMB2019},
  bibtex_show = {true},
  title = {PRISM: methylation pattern-based, reference-free inference of subclonal makeup},
  author = {Lee, Dohoon and Lee, Sangseon and Kim, Sun},
  journal = {Bioinformatics},
  volume = {35},
  number = {14},
  pages = {i520--i529},
  year = {2019},
  publisher = {Oxford University Press},
  html = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612819},
  pdf = {},
  selected = {true},
  presentation = {https://www.youtube.com/watch?v=Ii8YDjqNbL0}
}

Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches

Lee, Dohoon, Park, Youngjune, and Kim, Sun

Briefings in bioinformatics 2021

Bib HTML PDF

@article{lee2021towards,
  title = {Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches},
  author = {Lee, Dohoon and Park, Youngjune and Kim, Sun},
  journal = {Briefings in bioinformatics},
  volume = {22},
  number = {3},
  pages = {bbaa188},
  year = {2021},
  publisher = {Oxford University Press},
  html = {https://pubmed.ncbi.nlm.nih.gov/34020548/},
  pdf = {},
  selected = {true},
  bibtex_show = {true}
}

Learning the histone codes of gene regulation with large genomic windows and three-dimensional chromatin interactions using transformer

Lee, Dohoon, Yang, Jeewon, and Kim, Sun

bioRxiv 2021

Bib HTML Code Presentation

@article{Lee2021.12.30.472333,
  bibtex_show = {true},
  title = {Learning the histone codes of gene regulation with large genomic windows and three-dimensional chromatin interactions using transformer},
  author = {Lee, Dohoon and Yang, Jeewon and Kim, Sun},
  doi = {10.1101/2021.12.30.472333},
  journal = {bioRxiv},
  publisher = {Cold Spring Harbor Laboratory},
  html = {https://www.biorxiv.org/content/early/2021/12/30/2021.12.30.472333},
  code = {https://github.com/dohlee/chromoformer},
  presentation = {https://youtu.be/PfKabJ7iHJo},
  selected = {true},
  year = {2021}
}