生物資訊及系統生物研究所

2025

Caps-ac4C: An effective computational framework for identifying N4-acetylcytidine sites in human mRNA based on deep learning

Yao, L., Xie, P., Dong, D., Guo, Y., Guan, J., Zhang, W., Chung, C. R., Zhao, Z., Chiang, Y. C. & Lee, T. Y., 15 3月 2025, 於: Journal of Molecular Biology. 437, 6, 168961.

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1 引文斯高帕斯（Scopus）

dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era

Yao, L., Guan, J., Xie, P., Chung, C. R., Zhao, Z., Dong, D., Guo, Y., Zhang, W., Deng, J., Pang, Y., Liu, Y., Peng, Y., Horng, J. T., Chiang, Y. C. & Lee, T. Y., 6 1月 2025, 於: Nucleic acids research. 53, D1, p. D364-D376

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DbPTM 2025 update: Comprehensive integration of PTMs and proteomic data for advanced insights into cancer research

Chung, C. R., Tang, Y., Chiu, Y. P., Li, S., Hsieh, W. K., Yao, L., Chiang, Y. C., Pang, Y., Chen, G. T., Chou, K. C., Paik, Y. S., Tran, P. L., Lin, C. P., Kao, Y. M., Chen, Y. J., Chang, W. C., Hsu, J. B. K., Horng, J. T. & Lee, T. Y., 6 1月 2025, 於: Nucleic acids research. 53, D1, p. D377-D386

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StackDILI: Enhancing Drug-Induced Liver Injury Prediction through Stacking Strategy with Effective Molecular Representations

Guan, J., Dong, D., Xie, P., Zhao, Z., Guo, Y., Lee, T. Y., Yao, L. & Chiang, Y. C., 27 1月 2025, 於: Journal of Chemical Information and Modeling. 65, 2, p. 1027-1039 13 p.

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2024

ACP-CapsPred: An explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network

Yao, L., Xie, P., Guan, J., Chung, C. R., Zhang, W., Deng, J., Huang, Y., Chiang, Y. C. & Lee, T. Y., 1 9月 2024, 於: Briefings in Bioinformatics. 25, 5, bbae460.

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4 引文斯高帕斯（Scopus）

A hierarchical fusion strategy of deep learning networks for detection and segmentation of hepatocellular carcinoma from computed tomography images

Lee, I. C., Tsai, Y. P., Lin, Y. C., Chen, T. C., Yen, C. H., Chiu, N. C., Hwang, H. E., Liu, C. A., Huang, J. G., Lee, R. C., Chao, Y., Ho, S. Y. & Huang, Y. H., 12月 2024, 於: Cancer Imaging. 24, 1, 43.

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5 引文斯高帕斯（Scopus）

AMPActiPred: A three-stage framework for predicting antibacterial peptides and activity levels with deep forest

Yao, L., Guan, J., Xie, P., Chung, C. R., Deng, J., Huang, Y., Chiang, Y. C. & Lee, T. Y., 6月 2024, 於: Protein Science. 33, 6, e5006.

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11 引文斯高帕斯（Scopus）

An ensemble deep learning model for predicting minimum inhibitory concentrations of antimicrobial peptides against pathogenic bacteria

Chung, C. R., Chien, C. Y., Tang, Y., Wu, L. C., Hsu, J. B. K., Lu, J. J., Lee, T. Y., Bai, C. & Horng, J. T., 20 9月 2024, 於: iScience. 27, 9, 110718.

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2 引文斯高帕斯（Scopus）

An evolutionary learning-based method for identifying a circulating miRNA signature for breast cancer diagnosis prediction

Sathipati, S. Y., Tsai, M. J., Aimalla, N., Moat, L., Shukla, S. K., Allaire, P., Hebbring, S., Beheshti, A., Sharma, R. & Ho, S. Y., 1 3月 2024, 於: NAR Genomics and Bioinformatics. 6, 1, lqae022.

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5 引文斯高帕斯（Scopus）

A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy

Guan, J., Yao, L., Xie, P., Chung, C. R., Huang, Y., Chiang, Y. C. & Lee, T. Y., 1 5月 2024, 於: Briefings in Bioinformatics. 25, 3, bbae208.

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9 引文斯高帕斯（Scopus）

BRCC3 Regulation of ALK2 in Vascular Smooth Muscle Cells: Implication in Pulmonary Hypertension

Shen, H., Gao, Y., Ge, D., Tan, M., Yin, Q., Wade Wei, T. Y., He, F., Lee, T. Y., Li, Z., Chen, Y., Yang, Q., Liu, Z., Li, X., Chen, Z., Yang, Y., Zhang, Z., Thistlethwaite, P. A., Wang, J., Malhotra, A. & Yuan, J. X. J. 及其他2, Shyy, J. Y. J. & Gong, K., 9 7月 2024, 於: Circulation. 150, 2, p. 132-150 19 p.

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4 引文斯高帕斯（Scopus）

CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network

Yao, L., Xie, P., Guan, J., Chung, C. R., Huang, Y., Pang, Y., Wu, H., Chiang, Y. C. & Lee, T. Y., 22 7月 2024, 於: Journal of Chemical Information and Modeling. 64, 14, p. 5725-5736 12 p.

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3 引文斯高帕斯（Scopus）

Catalytic role of the enol ether intermediate in the intramolecular Stetter reaction: a computational perspective

Huang, G. T. & Yu, J. S. K., 26 3月 2024, 於: Physical Chemistry Chemical Physics. 26, 15, p. 11833-11853 21 p.

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CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H. T., Cheng, X., Choi, Y. K., Chu, J. W., Crowley, M. F., Cui, Q., Damjanovic, A., Deng, Y., Devereux, M., Ding, X., Feig, M. F. & Gao, J. 及其他53, Glowacki, D. R., Gonzales, J. E., Hamaneh, M. B., Harder, E. D., Hayes, R. L., Huang, J., Huang, Y., Hudson, P. S., Im, W., Islam, S. M., Jiang, W., Jones, M. R., Käser, S., Kearns, F. L., Kern, N. R., Klauda, J. B., Lazaridis, T., Lee, J., Lemkul, J. A., Liu, X., Luo, Y., MacKerell, A. D., Major, D. T., Meuwly, M., Nam, K., Nilsson, L., Ovchinnikov, V., Paci, E., Park, S., Pastor, R. W., Pittman, A. R., Post, C. B., Prasad, S., Pu, J., Qi, Y., Rathinavelan, T., Roe, D. R., Roux, B., Rowley, C. N., Shen, J., Simmonett, A. C., Sodt, A. J., Töpfer, K., Upadhyay, M., van der Vaart, A., Vazquez-Salazar, L. I., Venable, R. M., Warrensford, L. C., Woodcock, H. L., Wu, Y., Brooks, C. L., Brooks, B. R. & Karplus, M., 2024, (Accepted/In press) 於: Journal of Physical Chemistry B.

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17 引文斯高帕斯（Scopus）

DeepKlapred: A deep learning framework for identifying protein lysine lactylation sites via multi-view feature fusion

Guan, J., Xie, P., Dong, D., Liu, Q., Zhao, Z., Guo, Y., Zhang, Y., Lee, T. Y., Yao, L. & Chiang, Y. C., 12月 2024, 於: International Journal of Biological Macromolecules. 283, 137668.

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1 引文斯高帕斯（Scopus）

Developing a practical neurodevelopmental prediction model for targeting high-risk very preterm infants during visit after NICU: a retrospective national longitudinal cohort study

on behalf of the Taiwan Premature Infant Follow-up Network, 12月 2024, 於: BMC Medicine. 22, 1, 68.

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3 引文斯高帕斯（Scopus）

Development of an Adaptive Artifact Subspace Reconstruction Based on Hebbian/Anti-Hebbian Learning Networks for Enhancing BCI Performance

Tsai, B. Y., Diddi, S. V. S., Ko, L. W., Wang, S. J., Chang, C. Y. & Jung, T. P., 1 1月 2024, 於: IEEE Transactions on Neural Networks and Learning Systems. 35, 1, p. 348-361 14 p.

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9 引文斯高帕斯（Scopus）

Discovery of Novel Spike Inhibitors against SARS-CoV-2 Infection

Tai, L. T., Yeh, C. Y., Chang, Y. J., Liu, J. F., Hsu, K. C., Cheng, J. C. & Lu, C. H., 6月 2024, 於: International Journal Of Molecular Sciences. 25, 11, 6105.

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1 引文斯高帕斯（Scopus）

Discovery of Potent Dengue Virus NS2B-NS3 Protease Inhibitors Among Glycyrrhizic Acid Conjugates with Amino Acids and Dipeptides Esters

Lin, Y. F., Lai, H. C., Lin, C. S., Hung, P. Y., Kan, J. Y., Chiu, S. W., Lu, C. H., Petrova, S. F., Baltina, L. & Lin, C. W., 12月 2024, 於: Viruses. 16, 12, 1926.

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Exploring prognostic implications of miRNA signatures and telomere maintenance genes in kidney cancer

Yerukala Sathipati, S., Jeong, S., Sharma, P., Mayer, J., Sharma, R., Ho, S. Y. & Hebbring, S., 19 12月 2024, 於: Molecular Therapy Oncology. 32, 4, 200874.

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Glycyrrhizic acid conjugates with amino acid methyl esters target the main protease, exhibiting antiviral activity against wild-type and nirmatrelvir-resistant SARS-CoV-2 variants

Le, U. N. P., Chang, Y. J., Lu, C. H., Chen, Y., Su, W. C., Chao, S. T., Baltina, L. A., Petrova, S. F., Li, S. R., Hung, M. C., Lai, M. M. C., Baltina, L. A. & Lin, C. W., 7月 2024, 於: Antiviral Research. 227, 105920.

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Guided diffusion for molecular generation with interaction prompt

Wu, P., Du, H., Yan, Y., Lee, T. Y., Bai, C. & Wu, S., 1 5月 2024, 於: Briefings in Bioinformatics. 25, 3, bbae174.

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3 引文斯高帕斯（Scopus）

Human DCP1 is crucial for mRNA decapping and possesses paralog-specific gene regulating functions

Chen, T. W., Liao, H. W., Noble, M., Siao, J. Y., Cheng, Y. H., Chiang, W. C., Lo, Y. T. & Chang, C. T., 1 11月 2024, 於: eLife. 13

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1 引文斯高帕斯（Scopus）

Identifying Antitubercular Peptides via Deep Forest Architecture with Effective Feature Representation

Yao, L., Guan, J., Li, W., Chung, C. R., Deng, J., Chiang, Y. C. & Lee, T. Y., 30 1月 2024, 於: Analytical chemistry. 96, 4, p. 1538-1546 9 p.

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3 引文斯高帕斯（Scopus）

Inhibition of ADAM9 promotes the selective degradation of KRAS and sensitizes pancreatic cancers to chemotherapy

Huang, Y. K., Cheng, W. C., Kuo, T. T., Yang, J. C., Wu, Y. C., Wu, H. H., Lo, C. C., Hsieh, C. Y., Wong, S. C., Lu, C. H., Wu, W. L., Liu, S. J., Li, Y. C., Lin, C. C., Shen, C. N., Hung, M. C., Lin, J. T., Yeh, C. C. & Sher, Y. P., 3月 2024, 於: Nature Cancer. 5, 3, p. 400-419 20 p.

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7 引文斯高帕斯（Scopus）

Inhibition of dengue viruses by N-methylcytisine thio derivatives through targeting viral envelope protein and NS2B-NS3 protease

Lin, C. S., Lu, C. H., Lin, T. H., Kiu, Y. T., Kan, J. Y., Chang, Y. J., Hung, P. Y., Koval'skaya, A. V., Tsypyshev, D. O., Tsypysheva, I. P. & Lin, C. W., 1 2月 2024, 於: Bioorganic and Medicinal Chemistry Letters. 99, 129623.

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5 引文斯高帕斯（Scopus）

Interpretable Multi-Scale Deep Learning for RNA Methylation Analysis across Multiple Species

Wang, R., Chung, C. R. & Lee, T. Y., 3月 2024, 於: International Journal Of Molecular Sciences. 25, 5, 2869.

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2 引文斯高帕斯（Scopus）

KinPred-RNA—kinase activity inference and cancer type classification using machine learning on RNA-seq data

Zhang, Y., Yao, L., Chung, C. R., Huang, Y., Li, S., Zhang, W., Pang, Y. & Lee, T. Y., 19 4月 2024, 於: iScience. 27, 4, 109333.

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1 引文斯高帕斯（Scopus）

Machine Learning-Based Characterization and Identification of Tertiary Lymphoid Structures Using Spatial Transcriptomics Data

Li, S., Wang, Z., Huang, H. D. & Lee, T. Y., 4月 2024, 於: International Journal Of Molecular Sciences. 25, 7, 3887.

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2 引文斯高帕斯（Scopus）

Multi-epitope vaccine design of African swine fever virus considering T cell and B cell immunogenicity

Chen, T. Y., Ho, Y. J., Ko, F. Y., Wu, P. Y., Chang, C. J. & Ho, S. Y., 12月 2024, 於: AMB Express. 14, 1, 95.

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1 引文斯高帕斯（Scopus）

Multi-Omics Characterization of E3 Regulatory Patterns in Different Cancer Types

Li, Z., Wan, J., Li, S., Tang, Y., Lin, Y. C. D., Ni, J., Cai, X., Yu, J., Huang, H. D. & Lee, T. Y., 7月 2024, 於: International Journal Of Molecular Sciences. 25, 14, 7639.

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One-month daily and three-month weekly rifapentine plus isoniazid are comparable in completion rate and safety for latent tuberculosis infection in non-HIV Population: a randomized controlled trial

Huang, H. L., Lee, M. R., Lee, C. H., Cheng, M. H., Lu, P. L., Sheu, C. C., Wang, J. Y., Chong, I. W. & Yang, J. M., 11月 2024, 於: Clinical Microbiology and Infection. 30, 11, p. 1410-1417 8 p.

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4 引文斯高帕斯（Scopus）

PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters

Chow, C. N., Yang, C. W., Wu, N. Y., Wang, H. T., Tseng, K. C., Chiu, Y. H., Lee, T. Y. & Chang, W. C., 5 1月 2024, 於: Nucleic acids research. 52, D1, p. D1569-D1578

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34 引文斯高帕斯（Scopus）

Robust and Sustained STING Pathway Activation via Hydrogel-Based In Situ Vaccination for Cancer Immunotherapy

Cheng, S. L., Lee, H. M., Li, C. P., Lin, M. W., Chou, M. Y., Yen, Y. T., Wu, T. H., Lian, Y. C., Shih, Y. C., Chiang, C. S., Chen, T. W., Wan, D. & Chen, Y., 29 10月 2024, 於: ACS Nano. 18, 43, p. 29439-29456 18 p.

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4 引文斯高帕斯（Scopus）

Sputum bacterial microbiota signature as a surrogate for predicting disease progression of nontuberculous mycobacterial lung disease

Huang, H. L., Lin, C. H., Lee, M. R., Huang, W. C., Sheu, C. C., Cheng, M. H., Lu, P. L., Huang, C. H., Yeh, Y. T., Yang, J. M., Chong, I. W., Liao, Y. C. & Wang, J. Y., 12月 2024, 於: International Journal of Infectious Diseases. 149, 107085.

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Subdomain dynamics enable chemical chain reactions in non-ribosomal peptide synthetases

Sun, X., Alfermann, J., Li, H., Watkins, M. B., Chen, Y. T., Morrell, T. E., Mayerthaler, F., Wang, C. Y., Komatsuzaki, T., Chu, J. W., Ando, N., Mootz, H. D. & Yang, H., 2月 2024, 於: Nature Chemistry. 16, 2, p. 259-268 10 p.

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5 引文斯高帕斯（Scopus）

The impact of Lacticaseibacillus paracasei GMNL-143 toothpaste on gingivitis and oral microbiota in adults: a randomized, double-blind, crossover, placebo-controlled trial

Lee, M. K., Chen, I. H., Hsu, I. L., Tsai, W. H., Lee, T. Y., Jhong, J. H., Liu, B. C., Huang, T. Y., Lin, F. K., Chang, W. W. & Wu, J. H., 12月 2024, 於: BMC Oral Health. 24, 1, 477.

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1 引文斯高帕斯（Scopus）

Trajectory Statistical Learning of the Potential Mean of Force and Diffusion Coefficient from Molecular Dynamics Simulations

Chen, Y. T., Yang, H. & Chu, J. W., 11 1月 2024, 於: Journal of Physical Chemistry B. 128, 1, p. 56-66 11 p.

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2023

ABPCaps: A Novel Capsule Network-Based Method for the Prediction of Antibacterial Peptides

Yao, L., Pang, Y., Wan, J., Chung, C. R., Yu, J., Guan, J., Leung, C., Chiang, Y. C. & Lee, T. Y., 6月 2023, 於: Applied Sciences (Switzerland). 13, 12, 6965.

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7 引文斯高帕斯（Scopus）

Accelerating the Discovery of Anticancer Peptides through Deep Forest Architecture with Deep Graphical Representation

Yao, L., Li, W., Zhang, Y., Deng, J., Pang, Y., Huang, Y., Chung, C. R., Yu, J., Chiang, Y. C. & Lee, T. Y., 3月 2023, 於: International Journal Of Molecular Sciences. 24, 5, 4328.

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17 引文斯高帕斯（Scopus）

A genome-wide association study (GWAS) of the personality constructs in CPAI-2 in Taiwanese Hakka populations

Kao, P. Y., Chen, M. H., Chang, W. A., Pan, M. L., Shu, W. D., Jong, Y. J., Huang, H. D., Wang, C. Y., Chu, H. Y., Pan, C. T., Liu, Y. L. & Lin, Y. S., 2月 2023, 於: PLoS ONE. 18, 2 February, e0281903.

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A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology

Wang, Z., Pang, Y., Chung, C. R., Wang, H. Y., Cui, H., Chiang, Y. C., Horng, J. T., Lu, J. J. & Lee, T. Y., 1 11月 2023, 於: Briefings in Bioinformatics. 24, 6, bbad330.

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3 引文斯高帕斯（Scopus）

A Robust Drug–Target Interaction Prediction Framework with Capsule Network and Transfer Learning

Huang, Y., Huang, H. Y., Chen, Y., Lin, Y. C. D., Yao, L., Lin, T., Leng, J., Chang, Y., Zhang, Y., Zhu, Z., Ma, K., Cheng, Y. N., Lee, T. Y. & Huang, H. D., 9月 2023, 於: International Journal Of Molecular Sciences. 24, 18, 14061.

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11 引文斯高帕斯（Scopus）

Artificial intelligence-driven pan-cancer analysis reveals miRNA signatures for cancer stage prediction

Yerukala Sathipati, S., Tsai, M. J., Shukla, S. K. & Ho, S. Y., 13 7月 2023, 於: Human Genetics and Genomics Advances. 4, 3, 100190.

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17 引文斯高帕斯（Scopus）

Assessing Non-Specific Neck Pain through Pose Estimation from Images Based on Ensemble Learning

Kang, J. H., Hsieh, E. H., Lee, C. Y., Sun, Y. M., Lee, T. Y., Hsu, J. B. K. & Chang, T. H., 12月 2023, 於: Life. 13, 12, 2292.

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1 引文斯高帕斯（Scopus）

Combining virtual screening with cis-/trans-cleavage enzymatic assays effectively reveals broad-spectrum inhibitors that target the main proteases of SARS-CoV-2 and MERS-CoV

Chang, Y. J., Le, U. N. P., Liu, J. J., Li, S. R., Chao, S. T., Lai, H. C., Lin, Y. F., Hsu, K. C., Lu, C. H. & Lin, C. W., 8月 2023, 於: Antiviral Research. 216, 105653.

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3 引文斯高帕斯（Scopus）

Data-Driven Two-Stage Framework for Identification and Characterization of Different Antibiotic-Resistant Escherichia coli Isolates Based on Mass Spectrometry Data

Chung, C. R., Wang, H. Y., Yao, C. H., Wu, L. C., Lu, J. J., Horng, J. T. & Lee, T. Y., 5月 2023, 於: Microbiology spectrum. 11, 3

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5 引文斯高帕斯（Scopus）

DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning

Yao, L., Zhang, Y., Li, W., Chung, C. R., Guan, J., Zhang, W., Chiang, Y. C. & Lee, T. Y., 10月 2023, 於: Protein Science. 32, 10, e4758.

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17 引文斯高帕斯（Scopus）

DoSurvive: A webtool for investigating the prognostic power of a single or combined cancer biomarker

Wu, H. W., Wu, J. D., Yeh, Y. P., Wu, T. H., Chao, C. H., Wang, W. & Chen, T. W., 18 8月 2023, 於: iScience. 26, 8, 107269.

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2 引文斯高帕斯（Scopus）

Dual Effects of 3-epi-betulin from Daphniphyllum glaucescens in Suppressing SARS-CoV-2-Induced Inflammation and Inhibiting Virus Entry

Yeh, Y. J., Chao, T. L., Chang, Y. J., Chang, S. Y., Lu, C. H., Chao, C. H., Su, W. C., Tseng, C. P., Lai, M. M. C. & Cheng, J. C., 12月 2023, 於: International Journal Of Molecular Sciences. 24, 23, 17040.

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2 引文斯高帕斯（Scopus）

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