Publications

•         Lee J, Jang S-W, Lee B, Shin J, Gong J-R, Shin D. NetG2P: Network-based genotype-to-phenotype transformation identifies key signaling crosstalk for prognosis in pan-cancer study. BMC Biol 24, 85 (2026). 

•         Yoon HN, Kim JH, Gu D, Lee J, Kim SY, Kim HJ, Jeong J, Shin D, Jung YS, Chung MK, Lee SJ, Choi SY. Patient-derived 3D organoid platform for functional assessment of GPC3-targeted CAR T cell cytotoxic activity in head and neck squamous cell carcinoma. Oral Oncol. (2026) Jan;172:107814.

•        Jeong, H., Lee, J., Son, JY., Lee JK., Kang M., Cho S., Kim JH., Jeon Y., Lee JH., Shin D., Kim HR., Lee H. and Cheong H. ULK1 knockout suppresses pancreatic cancer progression by inhibiting autophagy and enhancing antitumor immunity. Exp Mol Med, 57, 2816–2832 (2025).

•        MR Lee*, SM Kang*, JH Lee*, SY Kong, YW Kim, YS Lee, HW Shon, GM Kang, JY Lee, SM Youn, DW Kwack, JY Park, SM Kim, WY Choi, JH Lee, D. Shin, IJ Kwon, SW Choi, Y Kim, "Organoid morphology-guided classification for oral cancer reveals prognosis", Cell Reports Medicine, 6(5), 102129,  (2025) (* The first three authors are equally contributed) (DK shin co-corresponding author)

•        Kim MA, Kim B, Jeon J, Lee J, Jang H, Baek M, Seo SU, Shin D, Dutta A, Lee KY. "Tousled-like kinase loss confers PARP inhibitor resistance in BRCA1-mutated cancers by impeding non-homologous end joining repair", Mol Med. 31(1):18 (2025) 

•         D. Shin, J.R. Gong, S.D. Jeong, Y. Cho, H-P. Kim, T-Y. Kim, and  K.-H. Cho, "Attractor landscape analysis reveals a reversion switch in the transition of colorectal tumorigenesis", Advanced Science, 12(8), 2412503.  (2025)  - Hot topics in Tumors and Cancer (Cover)

•        B. Lee and D. Shin, "Contrastive learning for enhancing feature extraction in anticancer peptides", Briefings in Bioinformatics, Volume 25, Issue 3, bbae220 (2024)

•        D. Shin and K.-H. Cho, "Critical transition and reversion of tumorigenesis", Experimental & Molecular Medicine, 55, 692-705 (2023)

•        J. I. Joo, M. Choi, S.-H. Jang, S. Choi, S.-M. Park, D. Shin, and K.-H. Cho, "Realizing cancer precision medicine by integrating systems biology and nanomaterial engineering", Advanced Materials, 32(35):e1906783 (2020)

•        B. Lee, D. Shin, S. P. Gross, and K.-H. Cho, "Combined positive and negative feedback allows modulation of neuronal oscillation frequency during sensory processing", Cell Reports, 25(6), 1548 (2018)

•        S.-Y. Yeo, K.-W. Lee, D. Shin*, S. An, K.-H. Cho, and S.-H. Kim, "A positive feedback loop bi-stably activates fibroblasts", Nature Communications, 9, 3016 (2018). (* The first three authors are equally contributed)

•        D. Shin, J. Lee, J.-R. Gong, and K.-H. Cho, “Percolation transition of cooperative mutational effects in colorectal tumorigenesis”, Nature Communications, 8, 1270 (2017)

•        Y. Kim, S. Choi, D. Shin, and K.-H. Cho, “Quantitative evaluation and reversion analysis of the attractor landscapes of an intracellular regulatory network for colorectal cancer”, BMC Systems Biology, 11, 45 (2017)

•        K.-H. Cho, S. Lee, D. Kim, D. Shin, J. I. Joo, and S.-M. Park, "Cancer reversion, a renewed challenge in systems biology", Current Opinion in Systems Biology, 2, 48 (2017).

•        K.-H. Cho, J. I. Joo, D. Shin, D. Kim, and S.-M. Park, "The reverse control of irreversible biological processes", WIREs Systems Biology and Medicine, 8, 366 (2016).

•        D. Shin, I. S. Kim, J. M. Lee, S.-Y. Shin, J.-H. Lee, S. H. Baek, and K.-H. Cho, "The hidden switches underlying RORalpha-mediated circuits that critically regulate uncontrolled cell proliferation", Journal of Molecular Cell Biology, 6, 338 (2014).

•        D. Shin and K.-H. Cho, "Recurrent connections form a phase-locking neuronal tuner for frequency-dependent selective communication", Scientific Reports (Nature Publishing Group), 3 (2223), 1-9 (2013).

•        K. Noh, K. S. Shin, D. Shin, J. Y. Hwang, J. S. Kim, J. H. Jang, C. K. Chung, J.S. Kwon, and K.-H. Cho, "Impaired coupling of local and global functional feedbacks underlies abnormal synchronization and negative symptoms of Schizophrenia", BMC Systems Biology, 7, 30 (2013).

•        K. Jhung, S.-H. Cho, J.-H. Jang, J. Y. Park, D. Shin, K. R. Kim, E. Lee, K.-H. Cho, S. K. An, "Small-world networks in individuals at ultra-high risk for psychosis and first-episode schizophrenia during a working memory task", Neuroscience Letter, 535, 35-39 (2013).

•       C.-Y. Dong, D. Shin, S. Joo, Y. Nam, K.-H. Cho, "Identification of feedback loops in neural networks based on multi-step Granger causality", Bioinformatics, 28, 2146 (2012).

•       J.-R. Kim, D. Shin, S.H. Jung, P. Heslop-Harrison, and K.-H. Cho, “A design principle underlying the synchronization of oscillations in cellular systems”, Journal of Cell Science, 123, 537 (2010).

•       H. Oymak, D. Shin, and J. Hong, “Time-Dependent Phonon-Assisted Tunneling through a Single-Molecular Device: Ricatti Matrix Approach”,

EPL (Europhysics Letters), 77, Art. No. 37005 (2007).

•       D. Shin, H. Oymak, and J. Hong, “Phonon-photon-assisted tunneling through an Aharonov-Bohm ring”, Journal of Physics Condensed Matter, 19(22), Art. No. 226211 (2007).

•       D. Shin and J. Hong, “Momentum filtering by photon-assisted tunneling in a connected Aharonov-Bohm ring”, Phys. Rev. B 72, 113307 (2005).

•       D. Shin and J. Hong, “Electron transport in the Aharonov-Bohm pump”, Phys. Rev. B 70, 073301 (2004).

•       M. D. Kim, D. Shin, and J. Hong, “Scalable quantum computing using persistent current qubits with Josephson junctions”, Physica E 18, 45 (2003).

•       M. D. Kim, D. Shin, and J. Hong, “Double-well potentials in current qubits”, Phys. Rev. B 68, 134513 (2003).