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책 공개 시험



*Co-first author, †Co-corresponding author


29. Park, J.G., Roh, P.R., Kang, M.W., Cho, S.W., Hwangbo, S.H., Jung, H.D., Kim, H.U., Kim, J.H., Yoo, J.S., Han, J.W., Jang, J.W., Choi, J.Y., Yoon, S.K., You, Y.K., Choi, H.J. † , Ryu, J.Y. † , Sung, P.S. † "Intrahepatic immunoglobulin a complex induces polarization of cancer-associated fibroblasts to matrix phenotypes in the tumor microenvironment of hepatocellular carcinoma", Hepatology, 10: 1097 (2024.2)

28. Kim, J.Y., Kim, B.K., Moh, S.H., Jang, G. †, Ryu, J.Y. † "Investigation of the General Molecular Mechanisms of Gallic Acid via Analyses of Its Transcriptome Profile", International Journal of Molecular Sciences, 25(4), 2303 (2024.2)


27. Kim, W.J., Lee, Y.J., Kim, H.U., Ryu, J.Y., Yang, J.E. and Lee, S.Y., "Genome-wide identification of overexpression and downregulation gene targets based on the sum of covariances of the outgoing reaction fluxes", Cell Systems, 14(11): 990-1001 (2023.11)

26. Cho, J.S.*, Yang, D.*, Prabowo, C.P.S., Ghiffary, M.R., Han, T.H., Choi, K.R., Moon, C.W., Zhou, H., Ryu, J.Y., Kim, H.U., and Lee, S.Y., "Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs", Nature Comm., 12: 173 (2023.4)

25. Kim, Y.J.*, Ryu, J.Y.*, Kim, H.U.* and Lee, S.Y., "Computational prediction of interactions between Paxlovid and prescription drugs", Proc. Natl. Acad. Sci. (PNAS), 120 (12), e2221857120 (2023.3)

24. Ryu, J.Y.†, Jang, W.D., Jang, J.D., Oh, K.S.†, "PredAOT: a computational framework for prediction of acute oral toxicity based on multiple random forest models", BMC Bioinformatics, BMC bioinformatics 24 (1), 1-10 (2022.2)


23. Lim, G., You, K.Y., Lee, J.H., Jeon, M.K., Lee, B.H., Ryu, J.Y.†, Oh, K.S.†,  "Identification and New Indication of Melanin-Concentrating Hormone Receptor 1 (MCHR1) Antagonist Derived from Machine Learning and Transcriptome-Based Drug Repositioning Approaches", International Journal of Molecular Sciences, 23 (7), 3807 (2022.3)

22. Ryu, J.Y.†, Lee, J.H., Lee, B.H., Song, J.S., Ahn, S., Oh, K.S.†, "PredMS: A random forest model for predicting metabolic stability of drug candidates in human liver microsomes", Bioinformatics, 38(2), 364-368 (2022.1)

21. Lim, G., Lim, C.J., Lee, J.H., Lee, B.H., Ryu, J.Y.†, Oh, K.S.†, "Identification of new target proteins of a Urotensin-II receptor antagonist using transcriptome-based drug repositioning approach", Sci. Rep., 11 (1), 1-10 (2021. 8)

20. Kim, Y.J.*, Ryu, J.Y.*, Kim, H.U.*, Jang, W.D., and Lee, S.Y., "A deep learning approach to evaluate the feasibility of enzymatic reactions generated by retrobiosynthesis", Biotechnol. J., 16(5):e2000605 (2021.5)

19. Shaker, B., Yu, M.S., Song J.S., Ahn. S, Ryu, J.Y., Oh, K.S., and Na, D., "LightBBB: computational prediction model of blood–brain-barrier penetration based on LightGBM", Bioinformatics, 37(8):1135-1139 (2021.5)


18. Lee, J.H., Seo, H.W., Ryu, J.Y., Lim, C.J., Yi, K.Y., Oh, K.S., and Lee, B,H., "KR-39038, a Novel GRK5 Inhibitor, Attenuates Cardiac Hypertrophy and Improves Cardiac Function in Heart Failure", Biomol. Ther. (Seoul). 28(5): 482–489 (2020. 9)


17. Ryu, J.Y.†, Lee, M.Y., Lee, J.H., Lee, B.H., Oh, K.S.†, "DeepHIT: a deep learning framework for prediction of hERG-induced cardiotoxicity", Bioinformatics, 36(10):3049-3055 (2020. 5)


16. Jang, W.D., Kim, T.Y., Kim, H.U., Shim, W.Y., Ryu, J.Y., Park, J.H., and Lee, S.Y. "Genomic and metabolic analysis of Komagataeibacter xylinus DSM 2325 producing bacterial cellulose nanofiber", Biotechnol. Bioeng., 116(12): 3372-3381 (2019. 12)

15. Yang, D.*, Yoo, S.M.*, Gu, C., Ryu, J.Y., Lee, J.E., and Lee, S.Y., "Expanded synthetic small regulatory RNA expression platforms for rapid and multiplex gene expression knockdown", Metab. Eng., 54: 180-190 (2019.7)


14. Ryu, J.Y., Kim, H.U. † and Lee, S.Y. †, "Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers", Proc. Natl. Acad. Sci. (PNAS) ( (2019.6)


13. Cho, J.S., Gu, C., Han, T.H., Ryu, J.Y., and Lee, S.Y., "Reconstruction of context-specific genome-scale metabolic models using multiomics data to study metabolic rewiring", Curr. Opin. Sys. Biol., 15: 1-11 (2019. 6)


12. Chae, T.U.*, Choi, S.Y.*, Ryu, J.Y., and Lee, S.Y. "Production of ethylene glycol from xylose by metabolically engineered Escherichia coli", AIChE J., 64(12): 4193-4200 (2018. 12)

11. Choi, K.R., Ryu, J.Y., and Lee, S.Y. "Revisiting statistical design and analysis in scientific research", Small, 14(40): 1802604 (1-8) (2018. 10)

10. Ryu, J.Y.*, Kim, H.U.*, and Lee, S.Y. "Deep learning improves prediction of drug–drug and drug–food interactions", Proc. Nat. Acad. Sci. (PNAS), 201803294: 1-8 (2018. 5)


9. Tong, T., Chen, S., Wang, L., Tang, Y., Ryu, J.Y., Jiang, S., Wu, X., Chen, C., Luo, J., Deng, Z., Li, Z., Lee, S.Y., and Chen, S. "Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria", Proc. Nat. Acad. Sci. (PNAS), 115(13): E2988-E2996 (2018. 3)


8. Ryu, J.Y.*, Kim, H.U.*, and Lee, S.Y. “Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism”, Proc. Nat. Acad. Sci. (PNAS), 114: E9740-E9749 (2017.10)


7. Jang, W.D., Hwang, J.H., Kim, H.U., Ryu, J.Y., and Lee, S.Y. “Bacterial cellulose as an example product for sustainable production and consumption”, Microb. Biotechnol., 10(5), p. 1181-1185 (2017)

6. Hur, W.*, Ryu, J.Y.*, Kim, H.U., Hong, S.W., Lee, E.B., Lee, S.Y.†, and Yoon, S.K. † “Systems approach to characterize the metabolism of liver cancer stem cells expressing CD133”, Sci. Rep., 7, 45557, doi: 10.1038/srep45557 (2017)

2013 - 2015

5. Ryu, J.Y., Kim, H.U., and Lee, S.Y. “Human genes with a greater number of transcript variants tend to show biological features of housekeeping and essential genes”, Mol. Biosyst., 11(10), p. 2798-2807, 2015.

4. Ryu, J.Y.*, Kim, H.U.*, and Lee, S.Y. “Reconstruction of genome-scale human metabolic models using omics data”, Integr. Biol., 7(8), p. 859-868, 2015.


3. Kim, H.U., Ryu, J.Y., Lee, J.O., and Lee, S.Y. “A systems approach to traditional oriental medicine”, Nature Biotechnol., 33, p. 264-268, 2015.


2. Song D.W., Lee, K.E., Ryu, J.Y., Jeon, H., and Kim, D.H. “The molecular interaction of heart LIM protein (HLP) with RyR2 and caveolin-3 is essential for Ca(2+)-induced Ca(2+) release in the heart”, Biochem. Biophys. Res. Commun., 463(4), p. 975-981, 2015.


1. Song, D.W., Ryu, J.Y., Kim, J.O., Kwon, E.J., and Kim, D.H. “The miR-19a/b family positively regulates cardiomyocyte hypertrophy by targeting atrogin-1 and MuRF-1”, Biochem. J. 457, p. 151–162, 2013.

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