Welcome

Hello. I'm a master's student studying computational biology, system biology, and deep learning in Life mining Lab, School of Life science, Gwangju Institute of Science and Technology (GIST), South Korea. I majored in life science and have taken a wide scope of courses including biology, mathematics, chemistry, computer science, and artificial intelligence at GIST college. My academic goal is to grow up into an independent scientist studying biophysics and protein drug design using in-silico approaches and to follow a career path to becoming a professor.

I have researched system biology and deep learning as follows :

Understanding cancer metabolism evolution with genome-scale modeling and anti-cancer drug target discovery.
Deep learning application with graph neural network in bacterial genome.

I'm interested in protein dynamics and de novo protein design :

De novo protein design
Protein-ligand, protein-protein, and protein-membrane interactions
Deciphering functional mechanisms of proteins
Drug delivery and discovery
Deep learning application

Email : jihun@gm.gist.ac.kr

Github : https://github.com/jihunni

Lab homepage : https://sites.google.com/view/gist-life-mining-lab/home

GIST homepage : https://www.gist.ac.kr/en/main.html

curriculum vitae

Education

Gwangju Institute of Science and Technology (GIST)

M.S Biology (2021.09 - 2023.08)
- 1st Topic : The construction of colorectal cancer metabolism evolution model and anti-cancer drug target discovery (2021.09 - present)
  - - Methods : Bioinformatics using Multi-omics (DNA-seq, RNA-seq, ATAC-seq), Network analysis, Genome-scale metabolic mode and Deep learning (Bidirectional Encoder Representations from Transformers, BERT)
- 2nd Topic : Bacterial genome function prediction with Graph neural network (2021.09 - 2022.10)
- 3rd Topic : The current advance in computer-aided drug design (Review article, 2022.11 - present)
  - - Contents : Force field, Optimization algorithm and sampling method, Molecular docking, Molecular dynamics, and De novo protein design
B.S Biology Major (2016.03 – 2021.08)

2nd thesis : The comprehensive molecular difference between male and female in hepatocellular carcinoma without viral hepatitis
- - Methods: Bioinformatic method with propensity score algorithm, differential gene expression analysis, gene set enrichment analysis, reporter metabolite analysis, pathway analysis, and protein expression analysis
  - Research Advisor: Sunjae Lee (Life Mining Lab, School of Life Science, GIST)
1st thesis : Novel anti-cancer drug discovery that inhibits the crosstalk between cancer cell, fibroblast and monocyte in tumor microenvironment
- - Methods : Experiment with Cell culture, collection of conditioned media, cell viability analysis, RT-qPCR
  - Research Advisor: Darren R. Williams (New Drug Target Discovery Lab, School of Life Science, GIST)

GIST college official transcript

GIST graduate school official transcript

University of California, Berkeley (summer session, 2017.06 – 2017.08)

Human genetics
Exploring the Brain: Introduction to Neuroscience

UC Berkeley Official Transcript

GIST - Caltech Collaboration course

Evolutionary Biology Course with Field Trip at Galapagos Island (2017.01)
Physical Biology of the Cell (2018.01)

Relevant Course

Biology

general biology
general biology - honor
general biology laboratory
molecular biology
advanced molecular biology
advanced biochemistry
cell biology
physiology
cell and developmental biology laboratory
biochemistry and molecular biology laboratory

evolutionary biology
human genetics
developmental biology
neuroscience
immunology
cancer biology
molecular biology of cancer
medial immunochemistry
bioinformatics

Physics and Chemistry

general chemistry
general chemistry experiment
general physics
general physics experiment
organic chemistry
biochemistry
physical chemistry (ongoing)
physical biology
modern advanced instrumental analysis

Mathematics

single-variable calculus -Honors
multi-variable calculus
linear algebra
differential equation
probability
statistics
numerical optimization
complex analysis (audit)

Computer Science

computer programming
data structure
database system
data science
high performance computing (parallel programming)

Artificial intelligence

statistical learning
machine learning
deep learning
natural language processing

Research

Computer Skills

Python

Pandas
Numpy
Tensorflow2
Pytorch
Pytorch geometric

bioinformatics system biology Statistics

Matlab

Statistics
Modeling
Optimization

SQL

MySQL
PostgreSQL

Linux

Principal Linux server management at Life mining Lab
(Ubuntu, CentOS7)

Bash shell script

Software development

BGCfinder

BGCfinder detects the biosynthetic gene clusters in bacterial genomes using deep learning. BGCfinder takes a fasta containing bacterial protein-coding sequences and converts them into graphs. Graph neural network takes the graphs to detect biosynthetic gene clusters. This work was accepted as a full paper at 16th International Conference on Data and Text Mining in Biomedical Informatics (DTMBIO), all of whose accepted full papers will be invited to BMC Bioinformatics on Jan 2023.

BGCfinder Link

Teaching experience

GS2004 Linear Algebra and Application (2021 Spring)

BS3112 Cell and Developmental Biology Laboratory (2022 Spring)

Animal ethics, mouse dissection and anatomy
pipetting, Techniques in mammalian cell culture
immunofluorescence staining
transient transfection and fluorescence microscopy
reporter gene (luciferase and beta-galactosidase assays)
primary isolation of mouse embryonic fibroblasts (MEFs)

BS3111 Biochemistry and Molecular Biology Laboratory (2022 Fall)

PCR Primer Design for Gene Cloning
PCR and Agarose Gel Electrophoresis
PCR purification and RE digestion of PCR product & vector.
Gel purification, DNA quantification and Ligation
Preparation of LB media & LB+Amp plates
Transformation into DH5α cells
Mini prep, RE digestion & Gel electrophoresis for sequencing
Transformation into BL21(DE3) cells
Small scale expression of the proteins, SDS-PAGE gel electrophoresis & Comassie blue staining
Large-scale overnight induction of the proteins
Purification of the Proteins
Validation of purified proteins, Protein quantitation, SDS-PAGE gels & Comassie blue staining

Awards & Scholarships

National Academic Scholarship, GIST (2021.09 - present)
Outstanding Undergraduate Research Award, School of Life Science, GIST (2021.08)
2020 Excellent Academic Books, Korean Academy of Sciences & Ministry of Education (2020.07.03)
National Science and Technology Scholarship, Korea government (2018.03 – 2021.08)
Academic Excellence Scholarship, GIST college (2017.09)
National Academic Scholarship, GIST college (2016.09 – 2019.06)

Publication and mass media

Field notes on the Galapagos Islands

Three GIST college students, who took GIST - Caltech collaboration course, explored the Galapagos islands to trace Darwin's theory of evolution. Through this book, we have shared our learning experiences and research in Galapagos Islands. It discussed the geological characteristics and the evolution mechanism in the Galapagos Islands. It also articulated the crisis of endangered species such as Galapagos giant tortoises and the importance of the ecology conservation project. This book was selected as an excellent academic book in 2020 by Korean Academy of Sciences and Ministry of Education

YTN science live Interview

YTN Science is a scientific broadcast news channel in South Korea. I was interviewed about the evolutionary biology and field trip to the Galapagos Islands at YTN Science. I explained the surprising research from Peter and Rosemary Grant, which was the first example of speciation observed by evolutionary biologists at Daphne Major.

Understanding the Many Causes of Cancer

Cancer is a major cause of death, and many resources are invested to develop new therapies for cancer. Sometimes the development of a new anti-cancer drug is announced in the news. However, science has not cured cancer and many people still die from cancer every day. Here is a question: what makes cancer difficult to cure?

In this science article, the myth related to cancer and the mechanism of cancer development were explained. It also discussed the biggest obstacles to cancer treatment and the current limitations of cancer treatment.

Link to this article

Translational Research is a Bridge

This article explained the importance and the roles of translational research. Generally, research in biomedical sciences can be divided into basic research and clinical research. Basic research reveals new knowledge about life, and clinical studies assess the eﬃcacy of new therapies.

Professor Euiheon Chung at the Department of Biomedical Science and Engineering (BMSE) at Gwangju Institute of Science and Technology, explained the concept of translational research. He mentioned "basic researchers are well trained to solve problems, but they cannot identify good problems. Clinical researchers have a lot of problems to solve, but they do not know how to solve them well. It is translational research that connects the two."