Publications

Publications in chronological order

Supervised Chemical Graph Mining Improves Drug-Induced Liver Injury (DILI) Prediction
Sangsoo Lim, Youngkuk Kim, Jeonghyeon Gu, Sunho Lee, and Sun Kim
iScience (Accepted) [link]
Multi-layer guilt-by-association-based drug repurposing by integrating clinical knowledge on biological heterogeneous networks
Dongmin Bang, Sangsoo Lim, Sangseon Lee, and Sun Kim
bioRxiv [link]
On modeling and utilizing chemical compound information with deep learning technologies: A task-oriented approach
Sangsoo Lim*, Sangseon Lee*, Yinhua Piao, MinGyu Choi, Dongmin Bang, Jeonghyeon Gu, Sun Kim
Computational and structural biotechnology journal (20), 2022 [link]
SREBP1c-PARP1 axis tunes anti-senescence activity of adipocytes and ameliorates metabolic imbalance in obesity
Gung Lee, Ye Young Kim, Hagoon Jang, Ji Seul Han, Hahn Nahmgoong, Yoon Jeong Park, Sang Mun Han, Changyun Cho, Sangsoo Lim, Jung-Ran Noh, Won Keun Oh, Chul-Ho Lee, Sun Kim, and Jae Bum Kim
Cell Metabolism 702-718. e5, 2022 [link]
Embedding of FDA Approved Drugs in Chemical Space Using Cascade Autoencoder with Metric Learning
Jungwoo Kim, Sangsoo Lim, Sangseon Lee, Changyun Cho, and Sun Kim
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
Minsu Kim, Sangseon Lee, Sangsoo Lim, Doh Young Lee and Sun Kim
Scientific reports 11(1), 2021 [link]
Spatial Regulation of Reactive Oxygen Species via G6PD in Brown Adipocytes Supports Thermogenic Function
Jee Hyung Sohn, Yul Ji, Chang-Yun Cho, Hahn Nahmgoong, Sangsoo Lim, Yong Geun Jeon, Sang Mun Han, Ji Seul Han, Isaac Park, Hyun-Woo Rhee, Sun Kim, Jae Bum Kim
Diabetes 70(12), 2021 [link]
BioVLAB-Cancer-Pharmacogenomics: Tumor Heterogeneity and Pharmacogenomics Analysis of Multi-omics Data from Tumor on the Cloud
Sungjoon Park, Dohoon Lee, Youngkuk Kim, Sangsoo Lim, Heejoon Chae and Sun Kim
Bioinformatics [link]
MONTI: A Multi-Omics Non---negative Tensor Decomposition Framework for Gene-Level Integrative Analysis
Inuk Jung, Minsu Kim, Sungmin Rhee, Sangsoo Lim, and Sun Kim
Frontiers in Genetics 12:682841, 2021 [link]
Construction of Condition-Specific Gene Regulatory Network using Kernel Canonical Correlation Analysis
Dabin Jeong, Sangsoo Lim, Sangseon Lee, Minsik Oh, Changyun Cho, Hyeju Seong, Woosuk Jung, Sun Kim
Frontiers in Genetics 12:652623, 2021 [link]
DNMT1 maintains metabolic fitness of adipocytes through acting as an epigenetic safeguard of mitochondrial dynamics
Yoon Jeong Park, Sangseon Lee*, Sangsoo Lim*, Hahn Nahmgoong, Yul Ji, Jin Young Huh, Assim A. Alfadda, Sun Kim, and Jae Bum Kim
Proceedings of the National Academy of Sciences 118(11), 2021 [link]
A review on compound-protein interaction prediction methods: Data,format, representation and model
Sangsoo Lim*, Yijinxiu Lu*, Chang Yun Cho, Inyoung Sung, Jungwoo Kim, Youngkuk Kim, Sungjoon Park and Sun Kim
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
Minsik Oh, Sungjoon Park, Sangseon Lee, Dohoon Lee, Sangsoo Lim, Dabin Jeong, Kyuri Jo, Inuk Jung and Sun Kim
Froniters in Genetics 11:564792, 2020 [link]
Cancer subtype classification and modeling by pathway attention and propagation
Sangseon Lee, Sangsoo Lim, Taeheon Lee, Inyoung Sung and Sun Kim
Bioinformatics 36(12), 2020 [link]
Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data
Sangsoo Lim, Sangseon Lee, Inuk Jung, Sungmin Rhee and Sun Kim
Briefings in Bioinformatics 20(1), 2020 [link]
Enhancer prediction with histone modification marks using a hybrid neural network model
Aeran Lim*, Sangsoo Lim*, Sun Kim (*equal contribution)
Methods 166, 2019 [link]
SpliceHetero: An information theoretic approach for measuring spliceomic intratumor heterogeneity from bulk tumor RNA-seq
Minsu Kim, Sangseon Lee, Sangsoo Lim and Sun Kim
PloS one 14(10), 2019 [link]
PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI
Ji Hwan Moon, Sangsoo Lim, Kyuri Jo, Sangseon Lee, Seokjun Seo and Sun Kim
BMC systems biology 11(2), 2017 [link]
Iterative segmented least square method for functional microRNA-mRNA module discovery in breast cancer
Sungmin Rhee, Sangsoo Lim and Sun Kim
International Journal of Data Mining and Bioinformatics, 2017 [link]
Measuring intratumor heterogeneity by network entropy using RNA-seq data
Youngjune Park, Sangsoo Lim, Jin-Wu Nam and Sun Kim
Scientific reports 6, 2016 [link]
Protein interaction network (pin)-based breast cancer subsystem identification and activation measurement for prognostic modeling
Sangsoo Lim, Youngjune Park, Benjamin Hur, Minsu Kim, Wonshik Han and Sun Kim
Methods 110, 2016 [link]
Information theoretic sub-network mining characterizes breast cancer subtypes in terms of cancer core mechanisms
Jinwoo Park, Benjamin Hur, Sungmin Rhee, Sangsoo Lim, Min-Su Kim, Kwangsoo Kim, Wonshik Han and Sun Kim
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
Sangsoo Lim, Dae Young Bang, Koon Ho Rha and Myeong Hee Moon
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
Ju Yong Lee, Sangsoo Lim, Sungha Park and Myeong Hee Moon
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
Ki Hun Kim, Ju Yong Lee, Sangsoo Lim and Myeong Hee Moon
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
Seul Kee Byeon, Ju Yong Lee, Sangsoo Lim, Donghoon Choi and Myeong Hee Moon
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
Sangsoo Lim, Seul Kee Byeon, Ju Yong Lee and Myeong Hee Moon
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
Dae Young Bang, Sangsoo Lim and Myeong Hee Moon
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
Rae Ung Jeong, Sangsoo Lim, Myoung Ok Kim and Myeong Hee Moon
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
Ju Yong Lee, Sangsoo Lim, Myeong-Hee Moon
Mass Spectrometry Letters 2(3), 2011 [link]
Shotgun lipidomics for candidate biomarkers of urinary phospholipids in prostate cancer
Hye Kyeong Min, Sangsoo Lim, Bong Chul Chung, Myeong Hee Moon
Analytical and bioanalytical chemistry 399(2), 2011 [link]