Research interests

1. Various clinical omics studies & precision medicine

   • next generation sequencing (NGS)-based mutation analysis to reveal genomic landscape or SNP markers of diseases

   • transcriptome analysis and identification of gene expression markers of diseases

   • pharmacogenomics study: development of computational models to predict drug response based on various types of markers

   • single cell RNA-seq analysis

   • metagenome analysis including microbiome, mycobiome and environmental metagenome

2. In silico drug discovery

   • structure-based virtual screening

   • machine learning-based quantitative structure-activity relationship (QSAR)

   • utilization of inverse virtual screening scores as properties of proteins. 

   • prediction of drug sensitivity

   • prediction of drug targets of a compound 

3. Development of prediction models and algorithms for various bioinformatics issues. 

   • development of pipelines to analyze tRNA expression profiles based on small RNA-seq such as miRNA-seq

   • prediction of protein abundances based on mRNA expression levels

4. Manipulating and improving genome-wide deletion library of fission yeast (S. pombe) as a tool for rapid identification of mode-of-action of compounds. 

Funded projects

In progress

• Korea Health Industry Development Institute (KHIDI), "Development of a pipeline analyzing serotypes of S. pneumoniae based on genomonics data" 100M, KRW, Apr 2022 - Dec 2023, Role: Principal Investigator

• National Research Foundation of Korea (NRF-2022R1A2C2093050), "Validation and Improvement of Machine Learning Models Predicting Effects of Anti-Cancer Drugs based on Single Cell RNA-Seq data analysis of Patient-derived Organoids", 894M KRW, Sep 2022 - Feb 2027, Role: Principal Investigator

Completed 

• National Research Foundation of Korea (NRF-2020M3C9A5086379), "Construction of pipeline to infer tRNA profiles and related analysis based on small RNA sequencing data stored in Korean public databases" 300M KRW, Jul 2020 - Dec 2021, Role: Principal Investigator

• National Research Foundation of Korea (NRF-2017M3A9B6061511), "Development of smart analysis pipeline of clinico-genomic data and drug target identification system"  690M KRW, Jun 2017 - Jun 2022, Role: Principal Investigator

• National Research Foundation of Korea (NRF-2017R1C1B2008617), "Development of the prediction model for variant-specific in vitro anticancer drug sensitivity using machine learning techniques" 400M KRW, Mar 2017 - Feb 2022, Role: Principal Investigator

• National Research Foundation of Korea (NRF-2017M3A9B6061511), "Analysis of mutual interference of genes in S.pombe deletion library" 297.5M KRW, Jun 2017 - Jun 2023, Role: Principal Investigator

• National Research Foundation of Korea (NRF-2020R1A4A3079570), "Discovery of biomarkers and therapeutic targets using deep learning based multi-omics for intractable aortic valve calcified disease" 1,333M KRW, Jul 2020- Feb 2023, Role: Co-investigator (PI: Min-Ho Oak, Mokpo National University)

• National Research Foundation of Korea (NRF-2017M3C9A6047615), "Open BIT integrative education program to produce genomics based precision medicine big-data analysis specialist"  961M KRW, Jun 2017 - Feb 2022, Role: Co-investigator (PI: Yeun-Jun Chung, The Catholic University of Korea School of Medicine)

• National Research Foundation of Korea (NRF-2014R1A1A2058647), "Construction of large-scale reverse docking profiles and application to prediction of protein function, druggability, and protein-protein interaction" 117M KRW, Nov 2014 - Apr 2017, Role: Principal Investigator

• National Research Foundation of Korea (NRF-2015M3C7A1064778), "Discovery of genetic variation markers specific to internet·game addiction in blood samples" 1,090M KRW, Oct 2015 - Sep 2019, Role: Co-investigator (PI: Yeun-Jun Chung, The Catholic University of Korea School of Medicine)

• National Research Foundation of Korea (NRF-2015M3C9A4053389), "Interdisciplinary BIT education program to produce clinico-genomic big-data analysis specialist" 512M KRW, Sep 2015  - Nov 2017,  Role: Co-investigator (PI: Yeun-Jun Chung, The Catholic University of Korea School of Medicine)