Academic Publication (SCI Journal Papers)
Academic Publication (SCI Journal Papers)
172. Lantian Yao, Feng Wang, Peilin Xie, Jiahui Guan, Zhihao Zhao, Xuxin He, Xingchen Liu, Ying-Chih Chiang*, Tzong-Yi Lee*, 2025 July, “StackPIP: An Effective Computational Framework for Accurate and Balanced Identification of Proinflammatory Peptides”, Journal of Chemical Information and Modeling, 65(14), 7777-7788. (SCI, IF: 5.7; 10/72 in CHEMISTRY, MEDICINAL)
171. Fung Ling Ng, Tsung-Chun Lin, Erick Wang, Tzong Yi Lee, Guan Ting Chen, Jiunn-Feng Su, Wen Liang Chen, 2025 July, “Bacillus-Based Biofertilizer Influences Soil Microbiome to Enhance Soil Health for Sustainable Agriculture”, Sustainability, 17(14), 6293. (SCI, IF: 2.9; 58/91 in GREEN & SUSTAINABLE SCIENCE & TECHNOLOGY)
170. Peilin Xie, Lantian Yao*, Jiahui Guan, Chia-Ru Chung, Zhihao Zhao, Feiyu Long, Zhenglong Sun, Tzong-Yi Lee*, Ying-Chih Chiang*, 2025 July, “ConsAMPHemo: A computational framework for predicting hemolysis of antimicrobial peptides based on machine learning approaches”, Protein Science, 34(7), e70087. (SCI, IF: 4.5; 76/313 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
169. Jiahui Guan, Lantian Yao, Peilin Xie, Zhihao Zhao, Dian Meng, Tzong-Yi Lee*, Junwen Wang*, Ying-Chih Chiang*, 2025 May, “Graph-RPI: predicting RNA–protein interactions via graph autoencoder and self-supervised learning strategies”, Briefings in Bioinformatics, 26(3), bbaf292. (SCI, IF: 6.8; 4/85 in BIOCHEMICAL RESEARCH METHODS)
168. Jiahui Guan, Peilin Xie, Dian Meng, Lantian Yao, Dan Yu, Ying-Chih Chiang, Tzong-Yi Lee*, Junwen Wang*, 2025 May, “ToxiPep: Peptide toxicity prediction via fusion of context-aware representation and atomic-level graph”, Computational and Structural Biotechnology Journal, 27, 2347-2358. (SCI, IF: 4.5; 82/313 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
167. Yuxuan Pang, Chunxuan Wang, Yao-zhong Zhang, Zhuo Wang, Seiya Imoto, Tzong-Yi Lee*, 2025 Mar, “STForte: tissue context-specific encoding and consistency-aware spatial imputation for spatially resolved transcriptomics”, Briefings in Bioinformatics, 26(2), bbaf174. (SCI, IF: 6.8; 4/85 in BIOCHEMICAL RESEARCH METHODS)
166. Peilin Xie, Jiahui Guan, Xuxin He, Zhihao Zhao, Yilin Guo, Zhenglong Sun, Lantian Yao, Tzong-Yi Lee*, Ying-Chih Chiang*, 2025 Feb, “CAP-m7G: A capsule network-based framework for specific RNA N7-methylguanosine site identification using image encoding and reconstruction layers”, Computational and Structural Biotechnology Journal, 27, 804-812. (SCI, IF: 4.5; 82/313 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
165. Lantian Yao, Peilin Xie, Danhong Dong, Yilin Guo, Jiahui Guan, Wenyang Zhang, Chia-Ru Chung, Zhihao Zhao, Ying-Chih Chiang*, Tzong-Yi Lee*, 2025 Jan, “Caps-ac4C: an effective computational framework for identifying N4-acetylcytidine sites in human mRNA based on deep learning”, Journal of Molecular Biology, 473(6), 168961. (SCI, IF: 4.7; 70/313 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
164. Jiahui Guan, Danhong Dong, Peilin Xie, Zhihao Zhao, Yilin Guo, Tzong-Yi Lee*, Lantian Yao*, Ying-Chih Chiang*, 2025 Jan, “StackDILI: Enhancing Drug-Induced Liver Injury Prediction through Stacking Strategy with Effective Molecular Representations”, Journal of Chemical Information and Modeling, 65(2), 1027-1039. (SCI, IF: 5.7; 10/72 in CHEMISTRY, MEDICINAL)
163. Lantian Yao, Jiahui Guan, Peilin Xie, Chia-Ru Chung, Zhihao Zhao, Danhong Dong, Yilin Guo, Wenyang Zhang, Junyang Deng, Yuxuan Pang, Yulan Liu, Yunlu Peng, Jorng-Tzong Horng, Ying-Chih Chiang* and Tzong-Yi Lee*, 2025 Jan, “dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era”, Nucleic Acids Research, gkae1019. (SCI, IF: 16.6; 6/313 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
162. Chia-Ru Chung‡, Yun Tang‡ (‡ joint first authorship), Yen-Peng Chiu, Shangfu Li, Wen-Kai Hsieh, Lantian Yao, Ying-Chih Chiang, Yuxuan Pang, Guan-Ting Chen, Kai-Chen Chou, You Sheng Paik, Tran Phuong Lam, Cheng-Pei Lin, Yu-Min Kao, Yi-Jie Chen, Wen-Chi Chang, Justin Bo-Kai Hsu, Jorng-Tzong Horng*, Tzong-Yi Lee*, 2025 Jan, “dbPTM 2025 update: Comprehensive Integration of PTMs and Proteomic Data for Advanced Insights into Cancer Research”, Nucleic Acids Research, gkae1005. (SCI, IF: 16.6; 6/313 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
161. Jiahui Guan, Peilin Xie, Danhong Dong, Qianchen Liu, Zhihao Zhao, Yilin Guo, Yilun Zhang, Tzong-Yi Lee*, Lantian Yao*, Ying-Chih Chiang*, 2024 Dec, “DeepKlapred: A deep learning framework for identifying protein lysine lactylation sites via multi-view feature fusion”, International Journal of Biological Macromolecules. (SCI, IF: 8.2; 35/285 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
160. Lantian Yao, Peilin Xie, Jiahui Guan, Chia-Ru Chung, Wenyang Zhang, Junyang Deng, Yixian Huang, Ying-Chih Chiang*, Tzong-Yi Lee*, 2024 Sept, “ACP-CapsPred: an explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network”, Briefings in Bioinformatics. (SCI, IF: 9.5; 3/77 in BIOCHEMICAL RESEARCH METHODS)
159. Chia-Ru Chung, Chung-Yu Chien, Yun Tang, Li-Ching Wu, Justin Bo-Kai Hsu, Jang-Jih Lu, Tzong-Yi Lee, Chen Bai, Jorng-Tzong Horng*, 2024 Aug, “An Ensemble Deep Learning Model for Predicting Minimum Inhibitory Concentrations of Antimicrobial Peptides Against Pathogenic Bacteria”, iScience. (SCI, IF: 5.8; 15/73 in MULTIDISCIPLINARY SCIENCES)
158. Zhongyan Li, Jingting Wan, Shangfu Li, Yun Tang, Yang-Chi-Dung Lin, Jie Ni, Xiaoxuan Cai, Jinhan Yu, Hsien-Da Huang, Tzong-Yi Lee*, 2024 Jul, “Multi-Omics Characterization of E3 Regulatory Patterns in Different Cancer Types”, International Journal of Molecular Sciences, 25(14), 7639. (SCI, IF: 5.6; 66/285 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
157. Lantian Yao, Peilin Xie, Jiahui Guan, Chia-Ru Chung, Yixian Huang, Yuxuan Pang, Huacong Wu, Ying-Chih Chiang, Tzong-Yi Lee*, 2024 Jul, “CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network”, Journal of Chemical Information and Modeling, 64(14), 5725-5736. (SCI, IF: 5.6; 10/72 in CHEMISTRY, MEDICINAL)
156. Lantian Yao, Jiahui Guan, Peilin Xie, Chia‐Ru Chung, Junyang Deng, Yixian Huang, Ying‐Chih Chiang, Tzong-Yi Lee*, 2024 Jun, “AMPActiPred: A three‐stage framework for predicting antibacterial peptides and activity levels with deep forest”, Protein Science, 33(6), e5006. (SCI, IF: 8; 36/285 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
155. Jiahui Guan, Lantian Yao, Peilin Xie, Chia-Ru Chung, Yixian Huang, Ying-Chih Chiang, Tzong-Yi Lee*, 2024 May, “A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy”, Briefings in Bioinformatics, 25 (3), bbae208. (SCI, IF: 9.5; 3/77 in BIOCHEMICAL RESEARCH METHODS)
154. Peng Wu, Huabin Du, Yingchao Yan, Tzong-Yi Lee, Chen Bai, Song Wu*, 2024 May, “Guided Diffusion for molecular generation with interaction prompt”, Briefings in Bioinformatics, 25 (3), bbae174. (SCI, IF: 9.5; 3/77 in BIOCHEMICAL RESEARCH METHODS)
153. Hui Shen, Ya Gao, Dedong Ge, Meng Tan, Qing Yin, Tong-You Wade Wei, Fangzhou He, Tzong-Yi Lee, Zhongyan Li, Yuqin Chen, Qifeng Yang, Zhangyu Liu, XinXin Li, Zixuan Chen, Yi Yang, Zhengang Zhang, Patricia Thistlethwaite, Jian Wang, Atul Malhotra, Jason Yuan, Kaizheng Gong, and John Shyy*, 2024, “BRCC3 Regulation of ALK2 in Vascular Smooth Muscle Cells: Implication in Pulmonary Hypertension”, Circulation, accepted. (SCI, IF: 37.8, CARDIAC & CARDIOVASCULAR SYSTEMS)
152. Lantian Yao, Jiahui Guan, Peilin Xie, Chia‐Ru Chung, Junyang Deng, Yixian Huang, Ying‐Chih Chiang*, Tzong‐Yi Lee*, 2024 June, “AMPActiPred: A three‐stage framework for predicting antibacterial peptides and activity levels with deep forest”, Protein Science 33 (6), e5006. (SCI, IF: 8.0; 36/285 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
151. Jiahui Guan, Lantian Yao, Peilin Xie, Chia-Ru Chung, Yixian Huang, Ying-Chih Chiang, Tzong-Yi Lee*, 2024 May, “A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy”, Briefings in Bioinformatics 25 (3), bbae208. (SCI, IF: 9.5; 3/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
150. Peng Wu, Huabin Du, Yingchao Yan, Tzong-Yi Lee*, Chen Bai*, Song Wu*, 2024 May, “Guided Diffusion for molecular generation with interaction prompt”, Briefings in Bioinformatics 25 (3), bbae174. (SCI, IF: 9.5; 3/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
149. Min-Kang Lee, I-Hui Chen, I-Ling Hsu, Wan-Hua Tsai, Tzong-Yi Lee, Jhih-Hua Jhong, Bai-Chia Liu, Tsui-Yin Huang, Fang-Kuei Lin, Wen-Wei Chang*, Ju-Hui Wu*, 2024 April, “The impact of Lacticaseibacillus paracasei GMNL-143 toothpaste on gingivitis and oral microbiota in adults: a randomized, double-blind, crossover, placebo-controlled trial”, BMC Oral Health, Vol. 24 (1), 477.
148. Yuntian Zhang, Lantian Yao, Chia-Ru Chung, Yixian Huang, Shangfu Li, Wenyang Zhang, Yuxuan Pang, Tzong-Yi Lee*, 2024 April, “KinPred-RNA-Kinase Activity Inference and Cancer Type Classification using Machine Learning on RNA-seq Data”, iScience, Vol. 27 (4), 109333. (SCI IF: 5.8)
147. Yi-Ran Xu, Jinglu Zhao, Hsi-Yuan Huang, Yang-Chi-Dung Lin, Tzong-Yi Lee, Hsien-Da Huang, Yi Yang, Yong-Fei Wang, 2024 April, “Recent insights into breast milk microRNA: their role as functional regulators” Frontiers in Nutrition 11, 1366435.
146. Songyun Li, Zhuo Wang, Hsien-Da Huang, Tzong-Yi Lee*, 2024 March, “Machine Learning-Based Characterization and Identification of Tertiary Lymphoid Structures Using Spatial Transcriptomics Data”, International Journal of Molecular Sciences, Vol. 25 (7), 3887. (SCI, IF: 6.208; 65/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
145. Rulan Wang, Chia-Ru Chung, Tzong-Yi Lee*, 2024 March, “Interpretable Multi-Scale Deep Learning for RNA Methylation Analysis across Multiple Species”, International Journal of Molecular Sciences, Vol. 25 (5), 2869. (SCI, IF: 6.208; 65/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
144. Lantian Yao, Jiahui Guan, Wenshuo Li, Chia-Ru Chung, Junyang Deng, Ying-Chih Chiang*, Tzong-Yi Lee*, 2024 Jan, ”Identifying Antitubercular Peptides via Deep Forest Architecture with Effective Feature Representation”, Analytical Chemistry, 96 (4), 1538-1546. (SCI, IF: 7.4; 7/86 in CHEMISTRY, ANALYTICAL)
143. Chi-Nga Chow, Chien-Wen Yang, Nai-Yun Wu, Hung-Teng Wang, Kuan-Chieh Tseng, Yu-Hsuan Chiu, Tzong-Yi Lee, Wen-Chi Chang*, 2024 Jan, “PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters”, Nucleic Acids Research, 52 (D1), D1569-D1578. (SCI, IF:14.9; 11/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
142. Zhuo Wang, Yuxuan Pang, Ziji Liang, Haodong Chen, Jiexin Pan, Meng Zhang, Tzong-Yi Lee, Hsien-Da Huang, Xingzhi Li, 2023 Dec, “COMPREHENSIVE ANALYSIS OF SINGLE-CELL RNA SEQUENCING DATA OF HUMAN BLADDER TISSUE SAMPLES IN NORMAL AND CANCER STATES, WITH AND WITHOUT ANTI-PD-1 TREATMENT”, MEDICINE 102 (52), 1-1. (SCI, IF: 1.6)
141. Jiahui Guan, Lantian Yao, Chia-Ru Chung, Peilin Xie, Yilun Zhang, Junyang Deng, Ying-Chih Chiang*, Tzong-Yi Lee*, 2023 Dec, “Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning”, Journal of Chemical Information and Modeling, 63 (24), 7886-7898. (SCI, IF: 5.6; 11/60 in CHEMISTRY MEDICINAL)
140. Jiunn-Horng Kang, En-Han Hsieh, Cheng-Yang Lee, Yi-Ming Sun, Tzong-Yi Lee, Justin Bo-Kai Hsu*, Tzu-Hao Chang*, 2023 Dec, Assessing Non-Specific Neck Pain through Pose Estimation from Images Based on Ensemble Learning, Life 13 (12), 2292. (SCI, IF: 3.2, 34/92 in BIOLOGY)
139. Zhuo Wang, Yuxuan Pang, Chia-Ru Chung, Hsin-Yao Wang, Haiyan Cui, Ying-Chih Chiang, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee*, 2023 Nov, “A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology”, Briefings in Bioinformatics 24 (6), bbad330. (SCI, IF: 9.5; 3/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
138. Chia-Ru Chung, Jhen-Ting Liou, Li-Ching Wu, Jorng-Tzong Horng, Tzong-Yi Lee*, 2023 Dec 15, “Multi-Label Classification and Features Investigation of Antimicrobial Peptides with Various Functional Classes”, iScience Vol. 26, 108250. (SCI IF: 5.8)
137. Yixian Huang, Hsi-Yuan Huang, Yigang Chen, Yang-Chi-Dung Lin, Lantian Yao, Tianxiu Lin, Junlin Leng, Yuan Chang, Yuntian Zhang, Zihao Zhu, Kun Ma, Yeong-Nan Cheng, Tzong-Yi Lee, Hsien-Da Huang*, 2023 Sep, “A Robust Drug–Target Interaction Prediction Framework with Capsule Network and Transfer Learning”, International Journal of Molecular Sciences 24 (18), 14061. (SCI, IF: 6.208; 65/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
136. Lantian Yao, Yuntian Zhang, Wenshuo Li, Chia‐Ru Chung, Jiahui Guan, Wenyang Zhang, Ying‐Chih Chiang*, Tzong-Yi Lee*, 2023 Aug, "DeepAFP: an effective computational framework for identifying antifungal peptides based on deep learning", Protein Science, e4758. (SCI, IF: 8.0; 36/285 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
135. Jiahui Guan, Lantian Yao, Chia-Ru Chung, Ying-Chih Chiang*, Tzong-Yi Lee*, 2023 June, "StackTHPred: Identifying Tumor-Homing Peptides through GBDT-Based Feature Selection with Stacking Ensemble Architecture", International Journal of Molecular Sciences, Vol. 24 (12), 10348. (SCI, IF: 6.208; 65/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
134. Lantian Yao, Yuxuan Pang, Jingting Wan, Chia-Ru Chung, Jinhan Yu, Jiahui Guan, Clement Leung, Ying-Chih Chiang*, Tzong-Yi Lee*, 2023 June, "ABPCaps: A Novel Capsule Network-Based Method for the Prediction of Antibacterial Peptides", Applied Sciences, Vol. 13 (12), 6965. (SCI)
133. Chia-Ru Chung, Hsin-Yao Wang, Chun-Han Yao, Li-Ching Wu, Jang-Jih Lu, Jorng-Tzong Horng*, Tzong-Yi Lee*, 2023 April 12, “Data-Driven Two-Stage Framework for Identification and Characterization of Different Antibiotic-Resistant Escherichia coli Isolates Based on Mass Spectrometry Data", Microbiology Spectrum, e03479-22. (SCI, IF:9.043)
132. Renfei Ma, Shangfu Li, Luca Parisi, Wenshuo Li, Hsien-Da Huang, Tzong-Yi Lee*, 2023, “Holistic similarity-based prediction of phosphorylation sites for understudied kinases”, Briefings in Bioinformatics, accepted. (SCI, IF: 13.994; 1/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
131. Lantian Yao, Wenshuo Li, Yuntian Zhang, Junyang Deng, Yuxuan Pang, Yixian Huang, Chia-Ru Chung, Jinhan Yu, Ying-Chih Chiang*, Tzong-Yi Lee*, 2023, “Accelerating the discovery of anticancer peptides through deep forest architecture with deep graphical representation”, International Journal of Molecular Sciences, accepted. (SCI, IF: 6.208; 65/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
130. Rulan Wang, Chia-Ru Chung, Hsien-Da Huang and Tzong-Yi Lee*, 2023, “Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences”, Briefings in Bioinformatics, accepted. (SCI, IF: 13.994; 1/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
129. Menqi Luo, His-Yuan Huang, Hsien-Da Huang* and Tzong-Yi Lee*, 2023 Jan, “Extraction of MicroRNA-target interaction from biomedical literature by deep learning approach”, Briefings in Bioinformatics, 24 (1), bbac497. (SCI, IF: 13.994; 1/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
128. Chia-Ru Chung, Hsin-Yao Wang, Po-Han Chou, Li-Ching Wu, Jang-Jih Lu, Jorng-Tzong Horng*, Tzong-Yi Lee*, 2023 Jan, “Towards Accurate Identification of Antibiotic-resistant Pathogens through the Ensembl of Multiple Preprocessing Methods based on MALDI-TOF Spectra”, International Journal of Molecular Sciences, 24 (2), 998. (SCI, IF: 6.208; 65/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
127. Yue Zhang, Mengqi Luo, Peng Wu, Song Wu, Tzong-Yi Lee* and Chen Bai*, 2022 Nov 5, “Application of Computational Biology and Artificial Intelligence in Drug Design”, International Journal of Molecular Sciences, 2022, 23(21), 13568. (SCI, IF: 6.208; 65/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
126. Yuxuan Pang, Lantian Yao, Jingyi Xu, Zhuo Wang and Tzong-Yi Lee*, 2022 Nov 3, “Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities”, Bioinformatics,38 (24), 5368-5374. (SCI, IF: 6.931, 3/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
125. Chi-Nga Chow, Kuan-Chieh Tseng, Ping-Fu Hou, Nai-Yun Wu, Tzong-Yi Lee, Wen-Chi Chang*, 2022 Sep 5, “Mysteries of gene regulation: Promoters are not the sole triggers of gene expression”, Computational and Structural Biotechnology Journal, Vol. 20, 2022, 4910-4920. (SCI, IF: 7.271)
124. Jia Meng, Zhixiang Zuo, Tzong-Yi Lee, Zexian Liu, Yufei Huang, 2022 Aug, "Editorial: Bioinformatics resources for understanding RNA modifications", Methods (San Diego, Calif.), Vol. 206, 53-55. (SCI, IF: 4.647)
123. Qiyang Wu, Tianyang Huang, Songyan Xia, Frank Otto, Tzong-Yi Lee, Hsien-Da Huang, Ying-Chih Chiang*, 2022 July, “On the force field optimisation of β -lactam cores using the force field Toolkit”, Journal of Computer-Aided Molecular Design, Vol. 36, 537–547 (2022). https://doi.org/10.1007/s10822-022-00464-3. (SCI, IF: 4.179)
122. Renfei Ma, Shangfu Li, Wenshuo Li, Lantian Yao, Hsien-Da Huang*, Tzong-Yi Lee*, 2022 July, “KinasePhos 3.0: Redesign and expansion of the prediction on kinase-specific phosphorylation sites”, Genomics, Proteomics & Bioinformatics, S1672-0229 (22) 00081-X. doi: 10.1016/j.gpb.2022.06.004. (SCI, IF: 7.691; 17/175 in GENETICS & HEREDITY)
121. Yuntian Zhang and Tzong-Yi Lee*, 2022 May, “Revealing the Immune Heterogeneity between Systemic Lupus Erythematosus and Rheumatoid Arthritis Based on Multi-Omics Data Analysis”, International Journal of Molecular Sciences, 2022, 23(9), 5166. (SCI, IF: 6.208; 65/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
120. Jiahong Zhang, Zhuo Wang, Hsin-Yao Wang, Chia-Ru Chung, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee*, 2022 Apr, “Rapid Antibiotic Resistance Serial Prediction in Staphylococcus aureus Based on Large-Scale MALDI-TOF Data by Applying XGBoost in Multi-Label Learning”, Frontiers in Microbiology, 13:853775. (SCI, IF:6.064; 28/137 in Microbiology)
119. Chunxuan Wang, Zhuo Wang, Hsin-Yao Wang, Chia-Ru Chung, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee*, 2022 Mar, “Large-Scale Samples Based Rapid Detection of Ciprofloxacin Resistance in Klebsiella pneumoniae Using Machine Learning Methods”, Frontiers in Microbiology, 13:853775. (SCI, IF:6.064; 28/137 in Microbiology)
118. Yheh-Hsia Luo, Jhih-Hua Jhong, Wan-Hua Tsai, Li-Chan Yang, Chia-Hsuan Chou, Tzong-Yi Lee, Yao-Tsung Yeh, Cheng-Hsieh Huang, Yueh-Hsia Luo, 2022 Feb, “Heat-Killed Lacticaseibacillus paracasei GMNL-653 Exerts Antiosteoporotic Effects by Restoring the Gut microbiota Dysbiosis in Ovariectomized Mice”, Frontiers in nutrition, 9: 804210. (SCI, IF: 6.590)
117. Jhih-Hua Jhong, Lantian Yao, Yuxuan Pang, Zhongyan Li, Chia-Ru Chung, Rulan Wang, Shangfu Li, Wenshuo Li, Mengqi Luo, Renfei Ma, Yuqi Huang, Xiaoning Zhu, Jiahong Zhang, Hexiang Feng, Qifan Cheng, Chunxuan Wang, Kun Xi, Li-Ching Wu, Tzu-Hao Chang, Jorng-Tzong Horng, Lizhe Zhu, Ying-Chih Chiang, Zhuo Wang, Tzong-Yi Lee*, 2022 Jan, “dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data”, Nucleic Acids Research, 50 (D1), D460-D470. (SCI, IF:19.160; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
116. Yigang Chen, Lantian Yao, Yun Tang, Jhih-Hua Jhong, Jingting Wan, Jingyue Chang, Shidong Cui, Yijun Luo, Xiaoxuan Cai, Wenshuo Li, Qi Chen, Hsi-Yuan Huang, Zhuo Wang, Weiming Chen, Tzu-Hao Chang, Fengxiang Wei, Tzong-Yi Lee*, Hsien-Da Huang*, 2022 Jan“CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers”, Nucleic Acids Research, 50 (D1), D93-D101. (SCI, IF: 19.160; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
115. Zhongyan Li, Shangfu Li, Mengqi Luo, Jhih-Hua Jhong, Wenshuo Li, Lantian Yao, Yuxuan Pang, Zhuo Wang, Rulan Wang, Renfei Ma, Jinhan Yu, Yuqi Huang, Xiaoning Zhu, Qifan Cheng, Hexiang Feng, Jiahong Zhang, Chunxuan Wang, Justin Bo-Kai Hsu, Wen-Chi Chang, Feng-Xiang Wei*, Hsien-Da Huang*, Tzong-Yi Lee*, “dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications”, Nucleic Acids Research, 2022 Jan 7, 50 (D1), D471-D479. (SCI, IF: 19.160; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
114. Hsi-Yuan Huang, Yang-Chi-Dung Lin, Shidong Cui, Yixian Huang, Yun Tang, Jiatong Xu, Jiayang Bao, Yulin Li, Jia Wen, Huali Zuo, Weijuan Wang, Jing Li, Jie Ni, Yini Ruan, Liping Li, Yidan Chen, Yueyang Xie, Zihao Zhu, Xiaoxuan Cai, Xinyi Chen, Lantian Yao, Yigang Chen, Yijun Luo, Shupeng LuXu, Mengqi Luo, Chih-Min Chiu, Kun Ma, Lizhe Zhu, Gui-Juan Cheng, Chen Bai, Ying-Chih Chiang, Liping Wang, Fengxiang Wei, Tzong-Yi Lee*, Hsien-Da Huang*, 2022 Jan, “miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions”, Nucleic Acids Research, 50 (D1), D222-D230. (SCI, IF: 19.160; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
113. Rulan Wang, Zhuo Wang, Zhongyan Li, Tzong-Yi Lee*, 2022 Jan, “Residue-Residue Contact Can Be a Potential Feature for the Prediction of Lysine Crotonylation Sites”, Frontiers in Genetics, 12:788467. (SCI, IF: 4.599)
112. Lizhi He, Jhih-Hua Jhong, Qi Chen, Kai-Yao Huang, Karin Strittmatter, Johannes Kreuzer, Michael DeRan, Xu Wu, Tzong-Yi Lee, Nikolai Slavov, Wilhelm Haas, Alexander G. Marneros, 2021, “Global characterization of macrophage polarization mechanisms and identification of M2-type polarization inhibitors”, Cell Reports, Vol. 37, Issue 5, 109955. (SCI, IF: 9.995)
111. Hsin-Yao Wang, Chia-Ru Chung, Chao-Jung Chen, Ko-Pei Lu, Yi-Ju Tseng, Tzu-Hao Chang, Min-Hsien Wu, Wan-Ting Huang, Ting-Wei Lin, Tsui-Ping Liu, Tzong-Yi Lee*, Jorng-Tzong Horng*, Jang-Jih Lu*, 2021, “Clinically Applicable System for Rapidly Predicting Enterococcus faecium Susceptibility to Vancomycin”, Microbiology Spectrum, Vol. 9, 3, e00913-21. (SCI, IF:9.043)
110. Yuxuan Pang, Zhuo Wang, Jhih-Hua Jhong, Tzong-Yi Lee*, 2021, “AVPIden: a new scheme for identification and functional prediction of Antiviral peptides based on machine learning method”, Briefings in Bioinformatics, 22(6), bbab263, (SCI, IF: 13.994; 1/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
109. Hsin-Yao Wang, Chia-Ru Chung, Zhuo Wang, Shangfu Li, Bo-Yu Chu, Jorng-Tzong Horng*, Jang-Jih Lu*, Tzong-Yi Lee*, 2021 May, "A large-scale investigation and identification of Methicillin-resistant Staphylococcus aureus based on peaks binning of Matrix-Assisted Laser Desorption Ionization-Time of Flight MS Spectra", Briefings in Bioinformatics, 22(3), bbaa138. (SCI, IF: 13.994; 1/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
108. Yue Han, Ming He, Traci Marin, Hui Shen, Wei-Ting Wang, Tzong-Yi Lee, Hsiao-Chin Hong, Zong-Lai Jiang, Theodore Garland, John Y-J Shyy, Brendan Gongol, Shu Chien*, 2021 May, “Roles of KLF4 and AMPK in the inhibition of glycolysis by pulsatile shear stress in endothelial cells", Proceedings of the National Academy of Sciences, 118(21), e2103982118. (SCI, IF:12.777; 8/73 in MULTIDISCIPLINARY SCIENCES)
107. Qi Chen, Jhih-Hua Jhong, Shangfu Li, Chien-Hsun Huang*, Tzong-Yi Lee*, 2021 March, “A Metagenomics-based Study on Functional Associations between Vaginal Microbiota and Phenotypes of HPV-Infected Patients”, Applied Microbiology, 7(4): 195. (SCI, IF: 3.69)
106. Zhuo Wang, Hsin-Yao Wang, Chia-Ru Chung, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee*, 2021 July, “Large-scale mass spectrometry data combined with demographics analysis rapidly predicts methicillin resistance in Staphylococcus aureus”, Briefings in Bioinformatics, 22(4), bbaa293. (SCI, IF: 13.994; 1/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
105. 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. (SCI, IF: 13.994; 1/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
104. Chia-Ru Chung, Zhuo Wang, Jing-Mei Weng, Hsin-Yao Wang, Li-Ching Wu, Yi-Ju Tseng, Chun-Hsien Chen, Jang-Jih Lu, Jorng-Tzong Horng*, Tzong-Yi Lee*, 2021, “MDRSA: a web based-tool for rapid identification of multidrug resistant Staphylococcus aureus based on matrix-assisted laser desorption ionization-time of flight mass spectrometry”, Frontiers in Microbiology, 3548. (SCI, IF:5.640; 28/137 in Microbiology)
103. Mengqi Luo, Zhongyan Li, Shangfu Li, Tzong-Yi Lee*, 2021, “A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction”, BMC Bioinformatics, 22, 507. (SCI IF: 3.169)
102. Justin Bo-Kai Hsu, Tzong-Yi Lee, Sho-Jen Cheng, Gilbert Aaron Lee, Yung-Chieh Chen, Nguyen Quoc Khanh Le, Shiu-Wen Huang, Duen-Pang Kuo, Yi-Tien Li, Tzu-Hao Chang, Cheng-Yu Chen, 2021, “Identification of Differentially Expressed Genes in Different Glioblastoma Regions and Their Association with Cancer Stem Cell Development and Temozolomide Response”, Journal of Personalized Medicine, 11 (11), 1047. (SCI, IF: 4.945)
101. Tzu-Hao Wang, Cheng-Yang Lee, Tzong-Yi Lee, Hsien-Da Huang, Justin Bo-Kai Hsu, Tzu-Hao Chang*, 2021, “Biomarker Identification through Multiomics Data Analysis of Prostate Cancer Prognostication Using a Deep Learning Model and Similarity Network Fusion”, Cancers, 13(11), 2528. (SCI, IF: 6.639; 51/242 in ONCOLOGY)
100. Yu Wan, Zhuo Wang and Tzong-Yi Lee*, 2021, “Incorporating Support Vector Machine with Sequential Minimal Optimization to Identify Anticancer Peptides”, BMC Bioinformatics, Vol. 22(1), 1 - 16. (SCI IF: 3.169)
99. Zhongyan Li, Siyu Chen, Jhih-Hua Jhong, Yuxuan Pang, Kai-Yao Huang, Shangfu Li, Tzong-Yi Lee*, 2021, “UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase–substrate interactions”, Database: The Journal of Biological Databases and Curation, Vol. 2021, baab010. (SCI, IF: 3.451; 14/58 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
98. Rulan Wang, Zhuo Wang, Hongfei Wang, Yuxuan Pang and Tzong-Yi Lee*, 2020, Characterization and identification of lysine crotonylation sites based on machine learning method on both plant and mammalian, Scientific Reports, 10, 20447. (SCI, IF: 4.379; 17/73 in MULTIDISCIPLINARY SCIENCES)
97. Kuan-Chieh Tseng, Guan-Zhen Li, Yu-Cheng Hung, Chi-Nga Chow, Nai-Yun Wu, Yi-Ying Chien, Han-Qin Zheng, Tzong-Yi Lee, Po-Li Kuo, Song-Bin Chang, Wen-Chi Chang*, 2020, "EXPath 2.0: An Updated Database for Integrating High-Throughput Gene Expression Data with Biological Pathways", Plant and Cell Physiology, 61(10), 1818-1827. (SCI, IF: 4.927; 25/235 in PLANT SCIENCES)
96. Chia-Ru Chung, Ya-Ping Chang, Yu-Lin Hsu, Siyu Chen, Li-Ching Wu, Jorng-Tzong Horng* and Tzong-Yi Lee*, 2020 Jun 29, “Incorporating hybrid models into lysine malonylation sites prediction on mammalian and plant proteins”, Scientific Reports, Vol. 10, 10541. (SCI, IF: 4.379; 17/73 in MULTIDISCIPLINARY SCIENCES)
95. Hui-Ju Kao, Van-Nui Nguyen, Kai-Yao Huang, Wen-Chi Chang, and Tzong-Yi Lee*, 2020 Jun 24, "SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites", Genomics, Proteomics & Bioinformatics, S1672-0229(20)30060-7. (SCI, IF: 7.691; 17/175 in GENETICS & HEREDITY)
94. Chia-Ru Chung, Ting-Rung Kuo, Li-Ching Wu, Tzong-Yi Lee*, and Jorng-Tzong Horng*, 2020 May, “Characterization and Identification of Antimicrobial Peptides with Different Functional Activities”, Briefings in Bioinformatics, Vol. 21 (3): 1098-1114. (SCI, IF: 13.994; 1/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
93. Tzong-Yi Lee, Dr Kai-Yao Huang, Mr Cheng-Hsiang Chuang, Tzu-Hao Chang*, 2020 May, “Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication”, Computational Biology and Chemistry, Vol.12; 87:107277. (SCI, IF: 2.877)
92. Vijesh Kumar Yadav, Tzong-Yi Lee, Justin Bo-Kai Hsu, Hsien-Da Huang, Wei-Chung Vivian Yang*, Tzu-Hao Chang*, 2020 April 21, “Computational analysis for identification of the extracellular matrix molecules involved in endometrial cancer progression”, PLoS ONE, 15(4): e0231594. (SCI, IF:3.234; 8/56 in MULTIDISCIPLINARY SCIENCES)
91. Kuan-Chieh Tseng, Yi-Fan Chiang-Hsieh, Hsuan Pai, Nai-Yun Wu, Han-Qin Zheng, Chi-Nga Chow, Tzong-Yi Lee, Song-Bin Chang, Na-Sheng Lin*, Wen-Chi Chang*, 2020 March 17, “sRIS: a small RNA illustration system for plant next-generation sequencing data analysis”, Plant and Cell Physiology, pcaa034. (SCI, IF: 4.927; 25/235 in PLANT SCIENCES)
90. Hongfei Wang, Zhuo Wang, Zhongyan Li and Tzong-Yi Lee*, 2020, “Incorporating Deep Learning with Word Embedding to Identify Plant Ubiquitylation Sites”, Frontiers in Cell and Developmental Biology, 2020; 8: 572195. (SCI, IF: 6.684; 6/41 in DEVELOPMENTAL BIOLOGY)
89. Chia-Ru Chung, Jhih-Hua Jhong, Zhuo Wang, Siyu Chen, Yu Wan, Jorng-Tzong Horng and Tzong-Yi Lee*, 2020 Feb 2, “Characterization and Identification of Natural Antimicrobial Peptides on Different Organisms”, International Journal of Molecular Sciences, Vol. 21(3), 986. (SCI, IF: 5.923; 67/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
88. 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, "miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database", Nucleic Acids Research, Vol. 48 (D1), D148-D154. (SCI, IF: 19.160; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
87. Tzong-Yi Lee*, Justin Bo-Kai Hsu, Tzu-Hao Chang, 2020 Jan, "Characterization and Identification of Protein S-Nitrosylation Sites Based on Tertiary Structures," International Journal of Bioscience, Biochemistry and Bioinformatics, Vol. 10, no. 1, pp. 15-25, 2020.
86. Hsin-Yao Wang, Wen-Chi Li, Kai-Yao Huang, Chia-Ru Chung, Jorng-Tzong Horng, Jen-Fu Hsu, Jang-Jih Lu* and Tzong-Yi Lee*, 2019 Dec, "Rapid Classification of Group B Streptococcus Serotypes based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry and Machine Learning Techniques", BMC Bioinformatics, Vol. 20 (Suppl 19): 703. (SCI IF: 3.242)
85. Kai-Yao Huang, Justin Bo-Kai Hsu, and Tzong-Yi Lee*, 2019 Nov, "Characterization and Identification of Lysine Succinylation Sites based on Deep Learning Method", Scientific Reports, Vol. 9, 16175. doi:10.1038/s41598-019-52552-4. (SCI, IF: 4.996; 17/73 in MULTIDISCIPLINARY SCIENCES)
84. Chia-Ru Chung, Hsin-Yao Wang, Frank Lien, Yi-Ju Tseng, Chun-Hsien Chen, Tzong-Yi Lee, Jorng-Tzong Horng*, and Jang-Jih Lu*, 2019 Sep, "Incorporating statistical test and machine intelligence into strain typing of Staphylococcus haemolyticus based on matrix-assisted laser desorption ionization-time of flight mass spectrometry", Frontiers in Microbiology, Vol. 10: 2120. (SCI, IF:5.640; 28/137 in Microbiology)
83. Hsin-Yao Wang, Chung-Chih Hung, Chun-Hsien Chen, Tzong-Yi Lee, Kai-Yao Huang, Hsiao-Chen Ning, Nan-Chang Lai, Ming-Hsiu Tsai, Li-Chuan Lu, Yi-Ju Tseng, and Jang-Jih Lu, 2019 Aug, “Increase Trichomonas vaginalis detection based on urine routine analysis through a machine learning approach”, Scientific Reports, Vol. 9 (1), 1074. (SCI, IF: 4.996; 17/73 in MULTIDISCIPLINARY SCIENCES)
82. Jim Shr-Jeng Leu, Tzong-Yi Lee, Shu-Wei Cheng, Meng-Ying Tsai, Yu-Shan Lin, Tzeon-Jye Chiou, Kai-Yao Huang, An-Na Chiang*, 2019 Jun, “Structural and functional characterization of β2-glycoprotein I domain 1 in anti-melanoma cell migration,” Cancer Science, 110(6):1974-1986. (SCI, IF: 6.716; 63/308 in ONCOLOGY)
81. Justin Bo-Kai Hsu, Tzu-Hao Chang, Gilbert Aaron Lee, Tzong-Yi Lee and Cheng-Yu Chen, 2019 Mar 20, "Identification of potential biomarkers related to glioma survival by gene expression profile analysis", BMC Medical Genomics, Vol. 11 (Suppl 7):34. (SCI, 2017 IF: 3.317)
80. Kai-Yao Huang, Hui-Ju Kao, Justin Bo-Kai Hsu, Shun-Long Weng and Tzong-Yi Lee*, 2019 Feb 4, " Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites", BMC Bioinformatics, Vol. 19 (Suppl 13): 384. (SCI IF: 3.242)
79. 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: 19.160; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
78. 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: 19.160; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
77. 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:19.160; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
76. Van-Nui Nguyen*, Huy-Khoi Do, Thi-Xuan Tran, Nguyen-Quoc-Khanh Le, Anh-Tu Le and Tzong-Yi Lee, 2019, "Exploiting Two-Layer Support Vector Machine to Predict Protein SUMOylation Sites", Proceedings of the International Conference, ICERA 2018, DOI: 10.1007/978-3-030-04792-4_43. (Book chapter in Advances in Engineering Research and Application)
75. Kai-Yao Huang, Hui-Ju Kao, Justin Bo-Kai Hsu, Shun-Long Weng and Tzong-Yi Lee*, 2019 Feb 4, " Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites", BMC Bioinformatics, Vol. 19 (Suppl 13): 384. (SCI IF: 3.242)
74. Hui-Ju Kao, Kai-Yao Huang and Tzong-Yi Lee*, 2018, “Exploiting Deep Learning Method to Identify Succinylated Sites on Lysine Residues”, International Conference on Bioinformatics, 26-28 September, 2018, India. (Selected for publication on Bioinformatics)
73. Shun-Long Weng†, Kai-Yao Huang† († joint first authorship), Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang* and Tzong-Yi Lee*, 2018 Nov 27, “Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes” Briefings in Bioinformatics, Vol. 19 (6):1102-1114. (SCI, IF: 13.994; 1/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
72. Hsin-Yao Wang, Chun-Hsien Chen, Tzong-Yi Lee, Jorng-Tzong Horng, Tsui-Ping Liu, Yi-Ju Tseng* and Jang-Jih Lu*, 2018, "Rapid Detection of Heterogeneous Vancomycin-Intermediate Staphylococcus aureus Based on Matrix-Assisted Laser Desorption Ionization Time-of-Flight: Using a Machine Learning Approach and Unbiased Validation", Frontiers in Microbiology, 9:2393. (SCI, 2020 IF:5.640; 28/137 in Microbiology)
71. Hsin-Yao Wang†, Shih-Cheng Chang†, Wan-Ying Lin†, Chun-Hsien Chen, Szu-Hsien Chiang, Kai-Yao Huang, Bo-Yu Chu, Jang-Jih Lu* and Tzong-Yi Lee*, 2018 Sep, "Machine learning-based method for obesity risk evaluation using single nucleotide polymorphisms derived from next-generation sequencing", Journal of Computational Biology. (SCI)
70. Chi-Nga Chow, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Han-Qin Zheng, Tzong-Yi Lee, Nai-Yun Wu, Kuan-Chieh Tseng, Ping-Fu Hou, and Wen-Chi Chang*, 2018, "Delineation of Condition Specific Cis- and Trans-acting Elements in Plant Promoters under Various Endo- and Exogenous Stimuli," BMC Genomics, Vol. 19 (Suppl 2):85. (SCI, 2016 IF: 3.729; 35/160 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)
69. Palmiro Poltronieria, Binlian Sun, Kai-Yao Huang, Tzu-Hao Chang, and Tzong-Yi Lee*, 2018, "State-of-the-art on viral microRNAs in HPV infection and cancer development," MicroRNA, Vol. 7, No. 2, 2018.
68. Hsin-Yao Wang‡, Tzong-Yi Lee‡ (‡ joint first authorship), Yi-Ju Tseng, Tsui-Ping Liu, Kai-Yao Huang, YungTa Chang, Chun-Hsien Chen*, Jang-Jih Lu*, March 2018, "A new scheme for strain typing of methicillin-resistant Staphylococcus aureus on the basis of matrix-assisted laser desorption ionization time-of-flight mass spectrometry by using machine learning approach," PLoS ONE, 13(3): e0194289. (SCI, IF:3.234; 8/56 in MULTIDISCIPLINARY SCIENCES)
67. Kai-Yao Huang†, Tzu-Hao Chang† († joint first authorship), Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K. Robert Lai and Tzong-Yi Lee*, 2017, "Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas," BMC Systems Biology, Vol. 11 (Suppl 7):131. (SCI, IF:2.303; 11/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
66. Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi and Tzong-Yi Lee*, 2017, "Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions," BMC Systems Biology, Vol. 11 (Suppl 7):132. (SCI, 2016 IF:2.303; 11/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
65. Hui-Ju Kao, Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Justin Bo-Kai Hsu, Chien-Hsun Huang* and Tzong-Yi Lee*, 2017, "MDD-Carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs," BMC Systems Biology, Vol. 11 (Suppl 7), 137. (SCI, 2016 IF:2.303; 11/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
64. Yi-Huang Hsueh*, Kai-Yao Huang, Sikhumbuzo Charles Kunene, and Tzong-Yi Lee*, 2017 Dec. 7, "Poly-γ-glutamic Acid Synthesis, Gene Regulation, Phylogenetic Relationships, and Role in Fermentation", International Journal of Molecular Sciences, Vol. 18(12). pii: E2644. (SCI, 2016 IF:3.226; 11/57 in CHEMISTRY, MULTIDISCIPLINARY)
63. Shun-Long Weng, Hui-Ju Kao, Chien-Hsun Huang*, Tzong-Yi Lee*, 2017, “MDD-Palm: Identification of protein S-palmitoylation sites with substrate motifs based on maximal dependence decomposition.” PLoS ONE, Vol. 12(6): e0179529. (SCI, IF:3.234; 8/56 in MULTIDISCIPLINARY SCIENCES)
62. Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Chien-Hsun Huang, Hui-Ju Kao, Tzu-Hao Chang, Hsin-Yao Wang, Jang-Jih Lu* and Tzong-Yi Lee*, 2017, “Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features,” BMC Bioinformatics, Vol. 18 (Suppl 3):16. (SCI, 2016 IF:2.448; 10/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
61. Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, K. Robert Lai* and Tzong-Yi Lee*, 2017, "A new scheme to characterize and identify protein ubiquitination sites," IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 14(2):393-403. (SCI, 2016 IF:1.955; 15/124 in STATISTICS & PROBABILITY)
60. Van-Nui Nguyen, Thi-Xuan Tran, Hai-Minh Nguyen, Hong-Tan Nguyen and Tzong-Yi Lee*, 2017, “A new schema to identify S-farnesyl cysteine prenylation sites with substrate motifs,” In: Akagi M., Nguyen TT., Vu DT., Phung TN., Huynh VN. (eds) Advances in Information and Communication Technology. ICTA 2016. Advances in Intelligent Systems and Computing, vol 538. Springer, Cham. (EI)
59. Kai-Yao Huang, Min-Gang Su, Hui-Ju Kao, Yun-Chung Hsieh, Jhih-Hua Jhong, Kuang-Hao Cheng, Hsien-Da Huang, Tzong-Yi Lee*, 2016, "dbPTM 2016: ten-year anniversary of a resource of post-translational modification of proteins" Nucleic Acids Research 2016 Jan. 4, Vol. 44(D1):D435-D446. (SCI, IF:16.971; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
58. Chi-Nga Chow, Han-Qin Zheng, Nai-Yun Wu, Chia-Hung Chien, Hsien-Da Huang, Tzong-Yi Lee, Yi-Fan Chian-Hsieh, Ping-Fu Hou, Tien-Yi Yang, and Wen-Chi Chang*, 2016, "PlantPAN 2.0: an update of Plant Promoter Analysis Navigator for reconstructing transcriptional regulatory networks in plants" Nucleic Acids Research 2016 Jan. 4; Vol. 44(D1):D1154-D1160. (SCI, IF:16.971; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
57. Van-Nui Nguyen, Kai-Yao Huang, Julia Tzu-Ya Weng, K. Robert Lai and Tzong-Yi Lee*, 2016, "UbiNet: an online resource for exploring functional associations and regulatory networks of protein ubiquitylation," DATABASE: The Journal of Biological Databases and Curation, 2016. pii: baw054. (SCI, 2016 IF: 3.290; 8/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
56. Van-Minh Bui, Shun-Long Weng, Cheng-Tsung Lu, Tzu-Hao Chang, Julia Tzu-Ya Weng and Tzong-Yi Lee*, 2016, "SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites," BMC Genomics, Vol. 17 (Suppl 1):9. (SCI, 2014 IF:3.986; 26/163 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)
55. Kai-Yao Huang, Julia Tzu-Ya Weng, Tzong-Yi Lee* and Shun-Long Weng*, 2016, "A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases," BMC Systems Biology, Vol. 10 (Suppl 1):3. (SCI, 2014 IF:2.435; 13/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
54. Chien-Hsun Huang, Min-Gang Su, Hui-Ju Kao, Jhih-Hua Jhong, Shun-Long Weng and Tzong-Yi Lee*, 2016, "Incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines," BMC Systems Biology, Vol. 10 (Suppl 1):6. (SCI, 2014 IF:2.435; 13/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
53. Shih-Wei Lee, Lawrence Shih-Hsin Wu, Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, and Julia Tzu-Ya Weng*, 2016, "Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis," BMC Bioinformatics, Vol. 17 (Suppl 1):3. (SCI, 2014 IF:2.576; 11/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
52. Van-Minh Bui, Cheng-Tsung Lu, Thi-Trang Ho, and Tzong-Yi Lee*, 2015, "MDD-SOH: Exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs" Bioinformatics, 2015 Sep. 26, pii: btv558. (SCI, IF: 7.307; 2/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
51. Hui-Ju Kao†, Chien-Hsun Huang† († joint first authorship), Neil Arvin Bretaña, Cheng-Tsung Lu, Kai-Yao Huang, Shun-Long Weng*, and Tzong-Yi Lee*, 2015, "A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs," BMC Bioinformatics, Vol. 16, Suppl 18, S10. (SCI, 2014 IF:2.576; 11/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
50. Yi-Ju Chen, Cheng-Tsung Lu, Kai-Yao Huang, Hsin-Yi Wu, Yu-Ju Chen*, Tzong-Yi Lee*, 2015, "GSHSite: exploiting an iteratively statistical method to identify S-glutathionylation sites with substrate specificity," PLoS ONE, Vol. 10 (4): e0118752. (SCI, 2014 IF:3.234; 8/56 in MULTIDISCIPLINARY SCIENCES)
49. Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, Tzu-Hao Chang, Neil Arvin Bretaña, K. Robert Lai, Julia Tzu-Ya Weng* and Tzong-Yi Lee*, "Characterization and Identification of Ubiquitin Conjugation Sites with E3 Ligase Recognition Specificities," BMC Bioinformatics, Vo. 16 (Suppl. 1), S1. (SCI, 2014 IF:2.576; 10/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
48. Yi-Ju Chen, Cheng-Tsung Lu, Min-Gang Su, Kai-Yao Huang, Wei-Chieh Ching, Hsiao-Hsiang Yang, Yen-Chen Liao, Yu-Ju Chen* and Tzong-Yi Lee*, 2015, "dbSNO 2.0: a resource for exploring structural environment, functional and disease associations, and regulatory networks of protein S-nitrosylation" Nucleic Acids Research Vol. 43 (D1): D503-11. (SCI, IF:16.971; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
47. Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, and Tzu-Ya Weng*, "An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients," BMC Bioinformatics, Vol. 16 (Suppl. 1), S5. (SCI, 2014 IF:2.576; 10/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
46. Kai-Yao Huang†, Tzong-Yi Lee († joint first authorship), Yu-Chuan Teng and Tzu-Hao Chang*, "ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors," BMC Bioinformatics, Vol. 16 (Suppl. 1), S9. (SCI, 2014 IF:2.576; 10/56 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
45. Tzu-Ya Weng, Li-Ching Wu, Wen-Chi Chang, Tzu-Hao Chang, Tatsuya Akutsu, and Tzong-Yi Lee*, 2014, "Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data," BioMed Research International, Vol. 2014, Article ID 814092, 3 pages. (SCI, 2013 IF:2.706; 53/165 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)
44. Hsin-Yi Wu, Cheng-Tsung Lu, Hui-Ju Kao, Yi-Ju chen, Tzong-Yi Lee* and Yu-Ju Chen*, 2014, "Characterization and identification of protein O-GlcNAcylation sites with substrate specificity," BMC Bioinformatics, Vol. 15 (Suppl 16), S1. (SCI, 2012 IF:3.024; 6/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
43. Yi-Ju Chen, Wei-Chieh Ching, Jinn-Shiun Chen, Tzong-Yi Lee, Cheng-Tsung Lu, Hsiao-Chiao Chou, Pei-Yi Lin, Kay-Hooi Khoo, Jenn-Han Chen and Yu-Ju Chen*, 2014, "Decoding the S-nitrosoproteomic Atlas in Individualized Human Colorectal Cancer Tissues Using a Label-free Quantitation Strategy," Journal of Proteome Research, Vol. 13 (11): 4942-58. (SCI, IF:5.001; 9/78 in BIOCHEMICAL RESEARCH METHODS)
42. Lawrence Shih-Hsin Wu, Shih-Wei Lee, Kai-Yao Huang, Tzong-Yi Lee, Paul Hsu, and Tzu-Ya Weng, 2014, "Systematic expression profiling analysis identifies specific microRNA-gene interactions that may differentiate between active and latent tuberculosis infection," BioMed Research International, Vol. 2014 (2014), Article ID 895179, 9 pages. (SCI, 2013 IF:2.706; 53/165 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)
41. Yi-Ju Chen, Cheng-Tsung Lu, Tzong-Yi Lee* and Yu-Ju Chen*, 2014, "dbGSH: a database of S-Glutathionylation" Bioinformatics, 2014 Aug 15;30(16):2386-8. (SCI, 2016 IF: 7.307; 2/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
40. Cheng-Tsung Lu†, Tzong-Yi Lee† († joint first authorship), Yu-Ju Chen, and Yi-Ju Chen*, 2014, "An intelligent system for identifying acetylated lysine on histones and non-histone proteins," Journal of Biomedicine and Biotechnology, Vol. 2014, Article ID 528650, 11 pages. (SCI, 2013 IF:2.706; 53/165 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)
39. Min-Gang Su, Chien-Hsun Huang, Tzong-Yi Lee, Yu-Ju Chen and Hsin-Yi Wu*, 2014, Incorporating amino acids composition and functional domains for identifying bacterial toxin proteins," Journal of Biomedicine and Biotechnology, Vol. 2014, Article ID 972692, 7 pages. (SCI, 2013 IF:2.706; 53/165 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)
38. Kai-Yao Huang, Hsin-Yi Wu, Yi-Ju Chen, Cheng-Tsung Lu, Min-Gang Su, Yun-Chung Hsieh, Chih-Ming Tsai, Kuo-I Lin, Hsien-Da Huang, Tzong-Yi Lee* and Yu-Ju Chen*, 2014, "RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals," DATABASE: The Journal of Biological Databases and Curation, 2014(0): bau034. (SCI, IF: 4.457; 5/52 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
37. Tzong-Yi Lee, Cheng-Wei Chang, Cheng-Tzung Lu, Tzu-Hsiu Cheng and Tzu-Hao Chang*, 2014, "Identification and characterization of lysine methylation sites on histones and non-histone proteins," Computational Biology and Chemistry, Vol. 50, June 2014, Pages 11–18. (SCI, 2013 IF:1.595; 32/83 in Biology)
36. Justin Bo-Kai Hsu, Kai-Yao Huang, Tzu-Ya Weng, Chien-Hsun Huang, Tzong-Yi Lee*, 2014, "Incorporating significant amino acid pairs and protein domains to identify RNA splicing related proteins with functional roles," Journal of Computer-Aided Molecular Design, Vol. 28 (1):49-60. (SCI, 2013 IF:2.782; 13/102 in COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS)
35. Min-Gang Su, Kai-Yao Huang, Cheng-Tsung Lu, Hui-Ju Kao, Ya-Han Chang and Tzong-Yi Lee*, 2014, "topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins," Nucleic Acids Research, Vol. 42 (D1): D537-D545. (SCI, IF:16.971; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
34. Kai-Yao Huang, Cheng-Tsung Lu, Neil Arvin Bretaña, Tzong-Yi Lee* and Tzu-Hao Chang*, 2013, "ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins", BMC Bioinformatics, Vol. 14 (Suppl 12), S10. (SCI, 2012 IF:3.024; 6/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
33. Min-Gang Su, Kai-Yao Huang, Chi-Hua Tung and Tzong-Yi Lee*, 2013, "A new scheme to predict phosphorylation sites on protein structures,"International Journal of Bioscience, Biochemistry and Bioinformatics (IJBBB), Vol. 3, No. 5, 473-478.
32. Cheng-Tsung Lu, Kai-Yao Huang, Neil Arvin Bretaña, Wen-Chi Chang and Tzong-Yi Lee*, 2013, "Exploiting two-layered support vector machine to predict phosphorylation sites on virus proteins," International Journal of Bioscience, Biochemistry and Bioinformatics (IJBBB), Vol. 3, No. 5, 460-465.
31. Min-Gang Su and Tzong-Yi Lee*, 2013, "Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures", BMC Bioinformatics, Vol. 14 (Suppl 16), S2. (SCI, 2012 IF:3.024; 6/47 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
30. Tzu-Hao Chang, Li-Ching Wu, Tzong-Yi Lee, Shu-Pin Chen, Hsien-Da Huang* and Jorng-Tzong Horng*, 2013, "EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC,"Journal of Computer-Aided Molecular Design, 27 (1):91-103. (SCI, 2012 IF:3.172; 11/99 in COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS)
29. Cheng-Tsung Lu, Kai-Yao Huang, Min-Gang Su, Tzong-Yi Lee*, Neil Arvin Bretaña, Wen-Chi Chang, Yi-Ju Chen, Yu-Ju Chen and Hsien-Da Huang*, 2013, "dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications," Nucleic Acids Research, 41 (D1):D295-305. (SCI, IF:16.971; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
28. Tzong-Yi Lee*, Yi-Ju Chen, Cheng-Tsung Lu, Wei-Chieh Ching, Yu-Chuan Teng, Hsien-Da Huang and Yu-Ju Chen*, 2012, "dbSNO: a database of cysteine S-Nitrosylation," Bioinformatics, 28(17):2293-5. (SCI, IF: 7.307; 2/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
27. Neil Arvin Bretaña, Cheng-Tsung Lu, Chiu-Yun Chiang, Min-Gang Su, Kai-Yao Huang, Tzong-Yi Lee* and Shun-Long Weng, 2012, "Identifying Protein Phosphorylation Sites with Kinase Substrate Specificity on Human Viruses," PLoS ONE, 7(7): e40694. (SCI, 2011 IF:4.092; 12/84 in BIOLOGY)
26. Tzong-Yi Lee*, Wen-Chi Chang*, Justin BK Hsu, Tzu-Hao Chang and Dray-Ming Shien, 2012, January "GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group," BMC Genomics, 13(Suppl 1):S3. (SCI, 2011 IF: 4.073; 26/157 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)
25. Cheng-Tsung Lu, Neil Arvin Bretaña, Tzu-Hsiu Cheng, and Tzong-Yi Lee*, 2011, "Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites," Journal of Computer-Aided Molecular Design, 25(10):987-95. (SCI, 2010 IF:3.374; 4/97 in COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS)
24. Justin Bo-Kai Hsu, Neil Arvin Bretaña, Tzong-Yi Lee* and Hsien-Da Huang*, 2011, "Incorporating evolutionary information and functional domains for identifying RNA splicing factors," PLoS ONE, 6(11): e27567. (SCI, 2010 IF:4.411; 12/85 in BIOLOGY)
23. Tzong-Yi Lee*, Cheng-Tsung Lu, Shu-An Chen, Neil Arvin Bretaña, Tzu-Hsiu Cheng, Min-Gang Su, and Kai-Yao Huang, 2011, "Investigation and identification of protein γ-glutamyl carboxylation sites," BMC Bioinformatics, 12 Suppl 11, S10. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
22. C.H. Chien, Y.M. Sun, W.C. Chang, P.Y. Chiang-Hsieh, Tzong-Yi Lee, W.C. Tsai, J.T. Horng, A.P. Tsou*, H.D. Huang*, 2011, "Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data," Nucleic Acids Research, 39(21):9345-9356. (SCI, IF:16.971; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
21. Justin Bo-Kai Hsu, Chih-Min Chiu, Sheng-Da Hsu, Wei-Yun Huang, Chia-Hung Chien, Tzong-Yi Lee and Hsien-Da Huang*, 2011, "miRTar: an integrated system for identifying miRNA-target interactions in Human," BMC Bioinformatics, 12:300. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
20. Tzong-Yi Lee*, Yi-Ju Chen, Tsung-Cheng Lu, Hsien-Da Huang and Yu-Ju Chen*, 2011, "SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity," PLoS ONE, 6(7): e21849. (SCI, 2010 IF:4.411; 12/85 in BIOLOGY)
19. Tzong-Yi Lee*, Neil ARVIN Bretana, and Cheng-Tsung Lu, 2011, "PlantPhos: using Maximal Dependence Decomposition to Identify Plant Phosphorylation Sites with Substrate Site Specificity," BMC Bioinformatics, 12:261. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
18. Tzong-Yi Lee*, Zong-Qing Lin, Sheng-Jen Hsieh, Neil Arvin Bretaña, and Cheng-Tsung Lu, 2011, "Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences," Bioinformatics, 27(13): 1780-1787. (SCI, IF: 7.307; 2/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
17. Shu-An Chen, Yu-Yen Ou, Tzong-Yi Lee and M. Michael Gromiha*, 2011, June "Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties," Bioinformatics, 27(15):2062-7. (SCI, IF: 7.307; 2/57 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
16. Tzong-Yi Lee*, Shu-An Chen, Hsin-Yi Hung, and Yu-Yen Ou, 2011, "Incorporating distant sequence features and radial basis function network to identify ubiquitin conjugation sites," PLoS ONE, 6(3): e17331. (SCI, 2010 IF:4.411; 12/85 in BIOLOGY)
15. Tzong-Yi Lee, Justin Bo-Kai Hsu, Wen-Chi Chang, and Hsien-Da Huang* , 2011, "RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans," Nucleic Acids Research, Vol. 39, D777-D787. (SCI, IF:16.971; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
14. Dray-Ming Shien, Tzong-Yi Lee, Wen-Chi Chang, Justin B.K. Hsu, Jorng-Tzong Horng, Po-Chian Hsu, Ting-Yuan Wang and Hsien-Da Huang*, 2010, "Incorporating Structural Characteristics for Identification of Protein Methylation Sites," Journal of Computational Chemistry, Vol. 30, No. 9, pp.1532-1543. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)
13. Shu-An Chen†, Tzong-Yi Lee<† († joint first authorship), and Yu-Yen Ou*, 2010, "Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins," BMC Bioinformatics, 11:536. (SCI, 2010 IF: 3.028; 4/37 in MATHEMATICAL & COMPUTATIONAL BIOLOGY)
12. Tzong-Yi Lee, Justin Bo-Kai Hsu, Feng-Mao Lin, Wen-Chi Chang, Po-Chiang Hsu, and Hsien-Da Huang, 2010, "N-Ace: using solvent accessibility and physicochemical properties to identify protein N-Acetylation sites," Journal of Computational Chemistry, Vol. 31 (15), 2759-2771. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY) (Cover Story)
11. D.M. Shien†, Tzong-Yi Lee† († joint first authorship), W.C. Chang, J.B.K. Hsu, J.T. Horng, P.C. Hsu, T.Y. Wang and H.D. Huang*, 2009, Jul 15 "Incorporating Structural Characteristics for Identification of Protein Methylation Sites," Journal of Computational Chemistry, Vol. 30, No. 9, pp.1532-1543. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)
10. W.C. Chang†, Tzong-Yi Lee† († joint first authorship), D.M. Shien, J. B.K. Hsu, P.C. Hsu, T.Y. Wang, J.T. Horng, H.D. Huang* and R.L. Pan*, 2009, Nov 30 "Incorporating support vector machine for identifying protein tyrosine sulfation sites," Journal of Computational Chemistry, . (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)
9. Tzong-Yi Lee, J.B.K. Hsu, W.C. Chang, T.Y. Wang, P.C. Hsu, and H.D. Huang*, 2009, "A Comprehensive Resource for Integrating and Displaying Protein Post-Translational Modifications," BMC Research Notes, 2(1):111.
8. W.C. Chang, Tzong-Yi Lee, H.D. Huang*, H.Y. Huang, R.L. Pan*, 2008, "PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group," BMC Genomics, 9:561. (SCI, 2010 IF: 4.206; 24/160 in BIOTECHNOLOGY & APPLIED MICROBIOLOGY)
7. Y.H. Wong†, Tzong-Yi Lee† († joint first authorship), H.K. Liang, C.M. Huang, Y.H. Yang, C.H. Chu, H.D. Huang* , M.T. Ko, and J.K. Hwang, 2007, "KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns," Nucleic Acids Research, Vol 35, W588-594. (SCI, IF:16.971; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
6. Tzong-Yi Lee, J.T. Horng, H.F. Juan, H.D. Huang, L.C. Wu, and F.M. Lin, 2006, "An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints," Journal of Computational Chemistry, Vol. 27, No. 9, 1020-32. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)
5. Tzong-Yi Lee, H.D. Huang*, J.H. Hung, Y.S. Yang, and T.H. Wang*, 2006, "dbPTM: An information repository of protein post-translational modification," Nucleic Acids Research, Vol. 34, D622-D627. (SCI, IF:16.971; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
4. J.H. Hung†, H.D. Huang†,* († joint first authorship), and Tzong-Yi Lee, "ProKware: an integrated software for presenting protein structural properties in protein tertiary structures," Nucleic Acids Research, Vol 34, W89-W94. (SCI, IF:16.971; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)
3. H.D. Huang*, Tzong-Yi Lee, S.W. Tseng, L.C. Wu, J.T. Horng, and A.P. Tsou, 2005, "Incorporating Hidden Markov Model for identifying protein kinase-specific phosphorylation sites," Journal of Computational Chemistry, Vol. 26, pp.1032-1041. (SCI, 2010 IF: 4.050; 27/144 in CHEMISTRY, MULTIDISCIPLINARY)
2. H.D. Huang, Tzong-Yi Lee, L.C. Wu, F.M. Lin, J.T. Horng, and A.P. Tsou, 2005, "MultiProtIdent: identifying proteins using database search and protein-protein interactions," Journal of Proteome Research, Vol. 4(3), 690-697. (SCI, 2010 IF: 5.460; 9/71 in BIOCHEMICAL RESEARCH METHODS)
1. H.D. Huang*, Tzong-Yi Lee, S.W. Tseng, and J.T. Horng, 2005, "KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites," Nucleic Acids Research, Vol. 33, W226-229. (SCI, IF:16.971; 8/298 in BIOCHEMISTRY & MOLECULAR BIOLOGY)