國內第一個以生物資訊研究及應用開發為主的頂尖研究中心，創立目標以跨領域研究為主軸

• 2002 – 生物資訊中心與生物資訊研究所同時成立（台灣首創）
• 2011 – 第二期教育部頂尖計畫成立為院級中心

1. Huang, K. W.; Liu, T. C.; Liang, R. Y.; Chu, L. Y.; Cheng, H. L.; Chu, J. W.; Hsiao, Y. Y.* Structural basis for overhang excision and terminal unwinding of DNA duplexes by TREX1. PLoS Biol 2018, 16, e2005653. PLoS Biol 2018, 16, e2005653.
2. Morrell, T. E., Rafalska-Metcalf, I. U., Yang, H., & Chu, J. W. (2018). Compound Molecular Logic in Accessing the Active Site of Mycobacterium tuberculosis Protein Tyrosine Phosphatase B. Journal of the American Chemical Society, 140(44), 14747-14752.

1. Lin, C. Y., Lee, C. H., Chuang, Y. H., Lee, J. Y., Chiu, Y. Y., Lee, Y. H. W., Jong, Y. J., Hwang, J. K., Huang, S. H., Chen, L. C., Wu, C. H., Tu, S. H., Ho, Y. S., Yang, J. M.* (2019) Membrane protein-regulated networks across human cancers, Nature Communications, 10(1):3131.
2. Kai-Yao Huang†, Tzong-Yi Lee*† († joint first authorship), Hui-Ju Kao, Chen-Tse Ma, Chao-Chun Lee, Tsai-Hsuan Lin, Wen-Chi Chang, Hsien-Da Huang*, 2019 Jan 8, “dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications”, Nucleic Acids Research, Vol. 47(D1): D298-D308. (SCI, IF: 14.9; Ranking: 10/285=3.5% in BIOCHEMISTRY & MOLECULAR BIOLOGY)
3. Chi-Nga Chow†, Tzong-Yi Lee† († joint first authorship), Yu-Cheng Hung, Guan-Zhen Li, Kuan-Chieh Tseng, Ya-Hsin Liu, Po-Li Kuo, Han-Qin Zheng, Wen-Chi Chang*, 2019 Jan 8, “PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants”, Nucleic Acids Research, Vol. 47(D1): D1155-D1163. (SCI, IF: 14.9; Ranking: 10/285=3.5% in BIOCHEMISTRY & MOLECULAR BIOLOGY) (ESI Highly Cited Paper)
4. Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li, Kai-Yao Huang, Sirjana Shrestha, Hsiao-Chin Hong, Yun Tang, Yi-Gang Chen, Chen-Nan Jin, Yuan Yu, Jia-Tong Xu, Yue-Ming Li, Xiao-Xuan Cai, Zhen-Yu Zhou, Xiao-Hang Chen, Yuan-Yuan Pei, Liang Hu, Jin-Jiang Su, Shi-Dong Cui, Fei Wang, Yue-Yang Xie, Si-Yuan Ding, Meng-Fan Luo, Chih-Hung Chou, Nai-Wen Chang, Kai-Wen Chen, Yu-Hsiang Cheng, Xin-Hong Wan, Wen-Lian Hsu, Tzong-Yi Lee*, Feng-Xiang Wei*, Hsien-Da Huang*, 2020 Jan 15, “miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database”, Nucleic Acids Research, Vol. 48 (D1), D148-D154. (SCI, IF: 14.9; Ranking: 10/285=3.5% in BIOCHEMISTRY & MOLECULAR BIOLOGY) (ESI Highly Cited Paper)

1. Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Tsai-Hsuan Lin, Kai-Yao Huang, Tzong-Yi Lee*, 2019 Jan 8, “dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data”, Nucleic Acids Research, Vol. 47(D1): D285-D297. (SCI, IF: 14.9; Ranking: 10/285=3.5% in BIOCHEMISTRY & MOLECULAR BIOLOGY)

1. Yuxuan Pang, Zhuo Wang, Jhih-Hua Jhong, Tzong-Yi Lee*, 2021 March, “Identifying anti-coronavirus peptides by incorporating different negative datasets and imbalanced learning strategies”, Briefings in Bioinformatics, 22 (2), 1085-1095. (IF: 9.5; Ranking: 3/77=3.9%, BIOCHEMICAL RESEARCH METHODS)

1. Chen, H. H.#, Hsueh, C. W.#, Lee, C. H.#, Hao, T. Y.#, Tu, T. Y., Chang, L. Y., Lee, J. C., Lin, C. Y.* (2023) SWEET: a single-sample network inference method for deciphering individual features in disease, Briefings in Bioinformatics, 24(2), bbad032. (IF: 9.5; Ranking: 3/77=3.9%, BIOCHEMICAL RESEARCH METHODS)
2. Chung, C. H., Lin, C. Y., Chen, C. Y., Hsueh, C. W., Chang, Y. W., Wang, C. C., Chu, P. Y., Tai, S. K., Yang, M. H.* (2023) Ferroptosis signature shapes the immune profiles to enhance the response to immune checkpoint inhibitors in head and neck cancer. Advanced Science, 10(15):e2204514. (IF: 15.1; Rank: 24/342=7.0%, MATERIALS SCIENCE, MULTIDISCIPLINARY)