International Journals/Conferences (*: Equal contributors)
- Piao Y, Lee S, Lee D, Kim S. Sparse Structure Learning via Graph Neural Networks for Inductive Document Classification. AAAI 2022. Accepted.
- Sung I*, Lee S*, Pak M, Shin Y, Kim S. AutoCoV: Learning the Spatial and Temporal Dynamics of COVID-19 Spread Patterns from Embedding Space by k-mer Based Deep Learning. BMC Medical Genomics, in revision.
- Kim J, Lim S, Lee S, Cho C, Kim S. Embedding of FDA Approved Drugs in Chemical Space Using Cascade Autoencoder with Metric Learning. IEEE BigComp 2022. AI-BioHealth 2022 workshop. Accepted.
- Kim I, Lee S, Kim Y, Namkoong H, Kim S. Probabilistic model for pathway-guided gene set selection. IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 12th International Workshop on Biomedical and Health Informatics (BHI 2021), Accepted.
- Kim MS, Lee S, Lim S, Lee DY, Kim S. Subnetwork Representation Learning for Discovering Network Biomarkers in Predicting Lymph Node Metastasis in Early Oral Cancer.. Scientific Reports, 2021 Dec; 11:23992.
- Lee T, Lee S, Kang M, Sun Kim. Deep Hierarchical Embedding for Simultaneous Modeling of GPCR Proteins in a Unified Metric Space. Scientific Reports, 2021 May; 11:9543.
- Lee S, Lee T, Noh YK, Kim S. Ranked k-spectrum kernel for comparative and evolutionary comparison of exons, introns, and CpG islands. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021 May; 18(30).
- Jeong D, Lim S, Lee S, Oh M, Cho C, Seong H, Jung W, Kim S. Construction of Condition-Specific Gene Regulatory Network using Kernel Canonical Correlation Analysis. Frontiers in Genetics, 2021 May; 12:652623.
- Moon JH, Lee S, Hur B, Kim S. MLDEG: A network-based ensemble model to identify differentially expressed genes consistently. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021 March; in press.
- Park YJ, Lee S*, Lim S*, Hahn N, Ji Y, Huh JY, Alfadda AA, Kim S, Kim JB. DNMT1 maintains metabolic fitness of adipocytes through acting as an epigenetic safeguard of mitochondrial dynamics. Proceedings of the National Academy of Sciences (PNAS). 2021 Mar 16; 118(11):e 2021073118.
- Oh M, Park S, Lee S, Lee D, Lim S, Jeong D, Jo K, Jung I, Kim S. DRIM: A web-based system for investigating drug response at the molecular level by condition-specific multi-omics data integration. Frontiers in Genetics, 2020 Nov; 11:564792.
- Kang M*, Lee S*, Lee D, Kim S. Learning Cell-Type-Specific Gene Regulation Mechanisms by Multi-Attention Based Deep Learning with Regulatory Latent Space. Frontiers in Genetics, 2020 Sep 30; 11:869.
- Lee S, Lim S, Lee T, Sung I, Kim S. Cancer subtype classification and modeling by pathway attention and propagation. Bioinformatics, 2020 Jun 15; 36(12):3818-3824.
- Lim S, Lee S, Jung I, Rhee S, Kim S. Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data. Briefings in Bioinformatics, 2020 Jan; 21(1):36-46.
- Hur B, Kang D, Lee S, Moon JH, Lee G, Kim S. Venn-diaNet: Venn diagram based network propagation analysis framework for computing multiple biological experiments. BMC Bioinformatics – Proceeding of 30th International Conference on Genome Informatics (GIW), 2019 Dec 27; 20(23):1-12.
- Kang D, Ahn H, Lee S, Lee CJ, Hur J, Jung W, Kim S. StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in Arabidopsis. BMC Genomics - Proceeding of 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), , 2019 Dec 20; 20(11):949.
- Kim MS, Lee S, Lim S, Kim S. SpliceHetero: An information theoretic approach for measuring spliceomic intratumor heterogeneity from bulk tumor RNA-seq. Plos ONE, 2019 Oct 23; 14(10).
- Lee DH. Lee S, Kim S. PRISM: Methylation Pattern-based, Reference-free Inference of Subclonal Makeup. Bioinformatics – Proceeding of 27th conference on Intelligent Systems for Molecular Biology (ISMB), 2019 Jul 5; 35(14):i520-i529.
- Lee CJ, Kang D, Lee S, Lee S, Kang J, Kim S. In silico experiment system for testing hypothesis on gene functions using three condition specific biological networks. Methods, 2018 May 25; 145:10-15.
- Lee S, Park Y, Kim S. MIDAS: Mining differentially activated subpaths of KEGG pathways from multi-class RNA-seq data. Methods, 2017 Jul 15; 124:13-24.
- Moon JH, Lim S, Jo K, Lee S, Seo S, Kim S, PINTnet: construction of condition-specic pathway interaction network by computing shortest paths on weighted PPI. BMC Systems Biology) – Proceeding of 15th Asia Pacific Bioinformatics Conference (APBC), 2017 Mar 14; 11(2):15.
- Lee S, Moon JH, Park Y, Kim S, Flow maximization analysis of cell cycle pathway activation status in breast cancer subtypes, IEEE International Conference on Big Data and Smart Computing (BigComp) 2017, Feb 13-16, Jeju, Korea.
- Chae H, Lee S, Nephew KP, Kim S, Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines. BMC Systems Biology – Proceeding of 27th International Conference on Genome Informatics (GIW), 2016 Dec 23; 10(4):116.
- Chae H, Lee S, Seo S, Jung D, Chang H, Nephew KP, Kim S. BioVLAB-mCpG-SNP-EXPRESS: A system for multi-level and multi-perspective analysis and exploration of DNA methylation, sequence variation (SNPs), and gene expression from multi-omics data. Methods, 2016 Jul 28; 111:64-71.
- Jeong HM, Lee S, Chae H, Kim R, Kwon MJ, Oh E, Choi YL, Kim S, Shin YK. Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis. Epigenomics, 2016 Jun 8; 8(8):1061-1077.
Book Chapters
- Pak M, Jeong D, Moon JH, Ann H, Hur B, Lee S, Kim S. Network Propagation for the Analysis of Multi-Omics Data. Recent Advances in Biological Network Analysis (pp. 185-217). 2021
Domestic Journal
- 박은화*, 이상선*, 김선. 신약개발과 맞춤의학을 위한 그래프 학습 기술. 한국정보과학회지 제 40권 제 3호, pp.30-40. 2022.
- 박은화, 이상선, 김선. 헬스케어 예측을 위한 전자 건강 기록 기반 그래프 컨볼루션 모델. 한국정보과학회 2020 한국컴퓨터종합학술대회 논문집, Vol.2020, pp.569-571. 2020 July.
- 강동원, 안홍렬, 이상선, 정우석, 김선. 시계열 유전자 발현 데이터의 스트레스 특이 반응 유전자 검출 및 스트레스 예측 알고리즘 개발. 한국정보과학회 2018 한국컴퓨터종합학술대회 논문집, Vol.2018, pp.1063-1065. 2018 Jun.