Research Interests

Next Generation Sequencing(NGS)

Cancer Genomics

Unraveling the biological mechanism of genes

Single-Cell RNA Sequencing

Education

Soongsil University

Seoul, Korea
Mar. 2015 - Feb. 2021
Bachelor of Science in School of Systems Biomedical Science(Bioengineering and Bioinformatics)

University of Mississippi

University, Mississippi, USA
Jan. 2019 - May 2019
Exchange Student, Biology

Korea University College of Medicine

Seoul, Korea
Mar. 2021 - Present
Biomedical Science

Personal Statement

    I am a diligent and honest graduate school student. I am interested in unraveling the mechanisms of cancer or disease using omics data including WES, Bulk RNA-sequencing, and Single cell RNA-sequencing data by utilizing various methodologies.
    My long-term goal is to be an expert in bioinformatics who studies disease or cancer-specific causal gene discovery. Through the graduate program, I am expected to do up-to-date research to accomplish my goal.

Relevant Experience

Choi Lab (Human Genetics and Genomics Lab), Korea University College of Medicine

Undergraduate Research Intern (Advisor : Jungmin Choi, Ph.D), Jul. 2020 - Feb. 2021
Graduate Student (Advisor : Jungmin Choi, Ph.D), Mar. 2021 - Present

  • Discovering the heterogeneous tumor microenvironment of gastric cancer patients using Single-cell RNA-sequencing
  • Transcriptional heterogeneity in hematopoietic stem cell niche with Single-cell RNA-sequencing data
  • Identifying the pseudogene-derived lncRNA biomarker responsible for the tumor progression and poor prognosis in liver cancer with transcriptomic data
  • Identification of biomarkers responsible for the metachronous gastric cancer progression
  • Discovery of master regulator affecting the resistance to the immunotherapy by the network analysis
  • Altered post-transcriptional modification at 3’-end in Yeast
  • Constructing pipeline for the alignment and variant calling of Whole genome sequencing data for the drug resistance inference and the construction of the phylogenetic tree

Post-Genome Informatics Lab, Soongsil University

Undergraduate Research Intern (Advisor : Sangsoo Kim, Ph.D), Aug. 2019 - Jul. 2020

Insilicogen, INC., Yongin, Korea

Internship, Jul. 2019 - Aug. 2019

  • Planned a personalized fruit and vegetable drink service referring to the personal genome data (prototype, via Neo4J)
   

   Click the Image to Open a powerpoint about the prototype project.

Publications

Identification of biomarkers responsible for the metachronous gastric cancer progression. in preparation

Miao R, Chun H,Gomes A. C, Choi J, & Pereira J.Competition between hematopoietic stem and progenitor cells controls hematopoietic stem cell compartment size. Nature Communications. 2022.

Lee J*, Hwang JH*, Chun H*, Woo W, Oh S, Choi J^, Kim LK^. PLEKHA8P1 Promotes Tumor Progression and Indicates Poor Prognosis of Liver Cancer. Int. J. Mol. Sci. 2021, 22, 7614


* : co-first Author

Teaching

CoRE (Collaboration Real Energy) Tutoring, Soongsil University

Tutor, Sep. 2019 - Dec. 2019, Subject: Distributed Big Data Computing

  • Taught Hadoop File System and PySpark to students for the whole semester

  • Taught python programming to students who are not accustomed to the python programming


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    Awards And Honors

    Semester Honor Scholarship(2016)

    Soongsil University

    CoRE Tutoring Best Tutor Award(2020)

    Center for Innovative Teaching and Learning, Soongsil University

    My Own Projects (During B.S)

    Identifying expression quantitative trait loci for pro-inflammatory response triggered by TIFA with genome- wide association study

    During the course (Practice of Biostatistics, 2019)
    @Soongsil University

    Click the Image to Open a pdf file.

    This study was conducted to identify eQTLs with 373 Europeans’ expression data of the genes encoding TIFA in Lymphoblastoid cell lines which were examined by the Geuvadis RNA-sequencing project. Overall analysis was operated with PLINK ver. 1.90. And Python programming and R were also used for the study.



    Drug repositioning and virtual screening against the calcium-dependent protein kinase1 (CDPK1) with SMINA

    During the course (Computational Molecular Biology and Lab., 2019)
    @Soongsil University

    Click the Image to Open a .ipynb

    This project was conducted to find stronger drug by molecular dynamic(MD) simulation. In order to find a feasible drug, I developed a customized scoring function and found candidate ligands to be docked with a receptor using DUDE, pubchem, and ZINC database.



    In silico analysis of gene expression and binding affinity to predict the susceptibility to Covid-19 in Pan-Cancer patients

    During the course (Undergraduate Thesis, 2020)
    @Soongsil University

    Click the Image to Open a pdf file.

    This thesis is mainly about predicting the susceptibility to Covid-19 in pan-cancer patients. With single nucleotide variation information of ACE2 gene, biding affinity between human ACE2 and SARS-CoV-2's spike protein.

    Rosalind

    During the Undergraduate

    Click the Image to Open my github repository.

    To improve the skill for using the python language, I solved the problems on the rosalind. By solving the various problems, I was able to learn various applications of the python for a genomics or other computational biology related studies.
    (Rank: 89/330, South Korea)