PRISM: Methylation Pattern-based, Reference-free Inference of Subclonal Makeup (ISMB 2019, Bioinformatics)
mirTime: Identifying Condition-Specific Targets of MicroRNA in Time-series Transcript Data using Gaussian Process Model and Spherical Vector Clustering (Bioinformatics 2019)
GABA-stimulated adipose-derived stem cells suppress subcutaneous adipose inflammation in obesity (PNAS, 2019)
DeepFam: Deep learning based alignment-free method for protein family modeling and prediction (ISMB 2018, Bioinformatics)
Hybrid Approach of Relation Network and Localized Graph Convolutional Filtering for Breast Cancer Subtype Classification (IJCAI 2017)
과제명: 멀티오믹스 분석 알고리즘 및 플랫폼 개발
연구비 지원기관: 한국연구재단 (과학기술정보통신부)
연구수행 기간: 2014.11.01 - 2022.10.31 (96개월)
과제명: 실험 및 문헌정보 거대 복잡형 데이터 통합분석추론 연구
연구비 지원기관: 한국연구재단 (과학기술정보통신부)
연구기간: 2017.9.1 - 2020.12.31 (40개월)

D. Kim*, Y. M. Sung*, J. Park*, S. Kim, J. Kim, J. Park, H. Ha, J. Y. Bae, S. Kim, and D. Baek, General Rules for Functional MicroRNA Targeting, Nature Genetics, 2016
D. Garcia*, D. Baek*#, C. Shin, G. Bell, A. Grimson, and D. Bartel#, Weak Seed-Pairing Stability and High Target-Site Abundance Decrease the Proficiency of lsy-6 and Other miRNAs, Nature Structural and Molecular Biology, 2011.
D. Baek*, J. Villen*, C. Shin*, F. Camargo, S. Gygi, and D. Bartel, The Impact of MicroRNAs on Protein Output, Nature, 2008.
D. Baek#, C. Davis, B. Ewing, D. Gordon, and P. Green#, Characterization and Predictive Discovery of Evolutionarily Conserved Mammalian Alternative Promoters, Genome Research, 2007.
D. Baek# and P. Green#, Sequence Conservation, Relative Isoform Frequencies, and Nonsense-Mediated Decay in Evolutionarily Conserved Alternative Splicing, Proceedings of the National Academy of Sciences U.S.A., 2005.
고정밀 암 진단을 위한 멀티오믹스 기반 유전체변이 발굴 및 진단용 소프트웨어 플랫폼 개발
당뇨합병증 정밀의료를 위한 엑소좀 다중오믹스 분석 플랫폼 개발

Mi Jeong Kwon, Sae Byul Lee, Jinil Han, Jeong Eon Lee, Jong Won Lee, Gyungyub Gong, Peter D. Beitsch, Seok Jin Nam, Sei Hyun Ahn, Byung-Ho Nam, Young Kee Shin. BCT score predicts chemotherapy benefit in Asian patients with mone receptor-positive, HER2-negative, lymph node-negative breast cancer. PLoS One. 2018 Nov 21;13(11):e0207155. doi: 10.1371/journal.pone.0207155. eCollection 2018
Han J, Choi YL, Kim H, Choi JY, Lee SK, Lee JE, Choi JS, Park S, Choi JS, Kim YD, Nam SJ, Nam BH, Kwon MJ, Shin YK. MMP11 and CD2 as Novel Prognostic Factors in Hormone Receptor-Negative, HER2-Positive Breast Cancer. Breast Cancer Res Treat. 2017 Apr 13. doi: 10.1007/s10549-017-4234-4. [Epub ahead of print]
Gong G, Kwon MJ, Han J, Lee HJ, Lee SK, Lee JE, Lee SH, Park S, Choi JS, Cho SY, Ahn SH, Lee JW, Cho SR, Moon Y, Nam BH, Nam SJ, Choi YL, Shin YK. A new molecular prognostic score for predicting the risk of distant metastasis in patients with HR+/HER2- early breast cancer. Scientific Reports. 2017 Mar 28;7:45554. doi: 10.1038/srep45554.
Oh E, Choi Y-L, Park T, Lee S, Nam SJ, Shin YK. A prognostic model for lymph node-negative breast cancer patients based on the integration of proliferation and immunity. Breast Cancer Res Treat. 2012 Apr;132(2):499-509. doi: 10.1007/s10549-011-1626-8

Genet Med. 2019 Dec;21(12):2695-2705. doi: 10.1038/s41436-019-0588-9.
Oncogenic effects of germline variants in lysosomal storage disease genes.
Sci Rep. 2019 Mar 5;9(1):3465. doi: 10.1038/s41598-019-39706-0.
Interpretation of EBV infection in pan-cancer genome considering viral life cycle: LiEB (Life cycle of Epstein-Barr virus).
Blood Cancer J. 2018 May 23;8(5):43. doi: 10.1038/s41408-018-0083-6.
RTK-RAS pathway mutation is enriched in myeloid sarcoma.

Atherogenic dyslipidemia promotes autoimmune follicular helper T cell responses via IL-27.
Nat Immunol. 2018 Jun;19(6):583-593. doi: 10.1038/s41590-018-0102-6
IL-27 confers a protumorigenic activity of regulatory T cells via CD39.
Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):3106-3111.
Fibrinogen cleavage products and Toll-like receptor 4 promote the generation of programmed cell death 1 ligand 2-positive dendritic cells in allergic asthma.
J Allergy Clin Immunol. 2018 Aug;142(2):530-541
Proatherogenic conditions promote autoimmune T helper 17 cell responses in vivo.
Immunity. 2014 Jan 16;40(1):153-65
Follicular regulatory T cells expressing Foxp3 and Bcl-6 suppress germinal center reactions.
Nat Med. 2011 Jul 24;17(8):983-8.