Postdoctoral Research Associate
(Available for a faculty position) I am currently a postdoctoral Research Associate affiliated with Bio & Health Informatics Lab and Bioinformatics Institute at Seoul National University. I received a Ph.D. degree in Bioinformatics at Seoul National University (advisor: Prof. Sun Kim) in 2019. My research currently focuses on developing machine learning algorithms to model toxicity of chemicals in large-scale drug discovery data, identifying toxicophores (hotspots) contributing to the toxicity of chemicals.
Education
Thesis title: “Quantification of pathway activity using RNA-seq data”
Advisor: Sun Kim
Research areas:
- transcriptome data analysis
- data mining
- computational modeling of biological data
Thesis title: “Development of computational algorithm for structural identification of phospholipids and profiling of phospholipid biomarkers for prostate cancer from human urine”
Advisor: Myeong Hee Moon
Research areas: Lipidomics, Proteomics, HPLC-MS, Asymmetrical Flow Field-Flow Fractionation
Received Bachelor of Science in Chemistry and Bachelor of Economics in Applied Statistics
Experiences
Awards
Title: A Supervised Markovian Random Walk Model for Investigating Hepatotoxicity Signatures of Chemical Drugs with Structural Alerts
Performance in HPLC experiments
Performance in GC experiments
grants
Publications
Publications in chronological order
Supervised Chemical Graph Mining Improves Drug-Induced Liver Injury (DILI) Prediction
iScience (Accepted) [link]
Multi-layer guilt-by-association-based drug repurposing by integrating clinical knowledge on biological heterogeneous networks
bioRxiv [link]
On modeling and utilizing chemical compound information with deep learning technologies: A task-oriented approach
Computational and structural biotechnology journal (20), 2022 [link]
SREBP1c-PARP1 axis tunes anti-senescence activity of adipocytes and ameliorates metabolic imbalance in obesity
Cell Metabolism 702-718. e5, 2022 [link]
Embedding of FDA Approved Drugs in Chemical Space Using Cascade Autoencoder with Metric Learning
2022 IEEE International Conference on Big Data and Smart Computing (BigComp), 2022 [link]
Subnetwork representation learning for discovering network biomarkers in predicting lymph node metastasis in early oral cancer
Scientific reports 11(1), 2021 [link]
Spatial Regulation of Reactive Oxygen Species via G6PD in Brown Adipocytes Supports Thermogenic Function
Diabetes 70(12), 2021 [link]
BioVLAB-Cancer-Pharmacogenomics: Tumor Heterogeneity and Pharmacogenomics Analysis of Multi-omics Data from Tumor on the Cloud
Bioinformatics [link]
MONTI: A Multi-Omics Non---negative Tensor Decomposition Framework for Gene-Level Integrative Analysis
Frontiers in Genetics 12:682841, 2021 [link]
Construction of Condition-Specific Gene Regulatory Network using Kernel Canonical Correlation Analysis
Frontiers in Genetics 12:652623, 2021 [link]
DNMT1 maintains metabolic fitness of adipocytes through acting as an epigenetic safeguard of mitochondrial dynamics
Proceedings of the National Academy of Sciences 118(11), 2021 [link]
A review on compound-protein interaction prediction methods: Data,format, representation and model
Computational and Structural Biotechnology Journal 19:1541-1556, 2021 [link]
DRIM: A web-based system for investigating drug response at the molecular level by condition-specific multi-omics data integration
Froniters in Genetics 11:564792, 2020 [link]
Cancer subtype classification and modeling by pathway attention and propagation
Bioinformatics 36(12), 2020 [link]
Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data
Briefings in Bioinformatics 20(1), 2020 [link]
Enhancer prediction with histone modification marks using a hybrid neural network model
Methods 166, 2019 [link]
SpliceHetero: An information theoretic approach for measuring spliceomic intratumor heterogeneity from bulk tumor RNA-seq
PloS one 14(10), 2019 [link]
PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI
BMC systems biology 11(2), 2017 [link]
Iterative segmented least square method for functional microRNA-mRNA module discovery in breast cancer
International Journal of Data Mining and Bioinformatics, 2017 [link]
Measuring intratumor heterogeneity by network entropy using RNA-seq data
Scientific reports 6, 2016 [link]
Protein interaction network (pin)-based breast cancer subsystem identification and activation measurement for prognostic modeling
Methods 110, 2016 [link]
Information theoretic sub-network mining characterizes breast cancer subtypes in terms of cancer core mechanisms
Journal of bioinformatics and computational biology 14(5), 2016 [link]
Rapid screening of phospholipid biomarker candidates from prostate cancer urine samples by multiple reaction monitoring of UPLC-ESI-MS/MS and statistical approaches
Bulletin of the Korean Chemical Society 35(4), 2014 [link]
Characterization of oxidized phospholipids in oxidatively modified low density lipoproteins by nanoflow liquid chromatography–tandem mass spectrometry
Journal of Chromatography A 1288, 2013 [link]
Top–down lipidomic analysis of human lipoproteins by chip-type asymmetrical flow field-flow fractionation–electrospray ionization-tandem mass spectrometry
Journal of Chromatography A 1280, 2013 [link]
Discovery of candidate phospholipid biomarkers in human lipoproteins with coronary artery disease by flow field-flow fractionation and nanoflow liquid chromatography–tandem mass spectrometry
Journal of Chromatography A 1270, 2012 [link]
Computational approach to structural identification of phospholipids using raw mass spectra from nanoflow liquid chromatography–electrospray ionization–tandem mass spectrometry
Journal of mass spectrometry 47(8), 2012 [link]
Effect of ionization modifiers on the simultaneous analysis of all classes of phospholipids by nanoflow liquid chromatography/tandem mass spectrometry in negative ion mode
Journal of Chromatography A 1240, 2012 [link]
Effect of D-allose on prostate cancer cell lines: phospholipid profiling by nanoflow liquid chromatography–tandem mass spectrometry
Analytical and bioanalytical chemistry 401(2), 2011 [link]
Effects of column length and particle diameter on phospholipid analysis by nanoflow liquid chromatography-electrospray ionization-mass spectrometry
Mass Spectrometry Letters 2(3), 2011 [link]
Shotgun lipidomics for candidate biomarkers of urinary phospholipids in prostate cancer
Analytical and bioanalytical chemistry 399(2), 2011 [link]
Patents
Patents listed in chronological order
LIPID ANALYSIS SYSTEM AND METHOD FOR ANALYSING THE LIPID
Korea registered [10-2015-0015756], 2015
Projects
List of currently leading/involved projects (under supervision by Professor Sun Kim)
Drug-Induced Liver Injury (DILI) Classification using Supervised Random Walk with Graph Pruning
- Manuscript under revision