Tzong-Yi Lee

94 papers C 6Journal 88
YearRankTypeTitle / Venue / Authors
2025 J jnl
AFPDeepPred: A Deep Learning Framework for Accurate Identification of Antifreeze Proteins.
J. Chem. Inf. Model.
Xingqiao Lin, Jiahui Guan, Feng Wang, Peilin Xie, Yiyang Zhao, Zhihao Zhao, Mingyi Xiang, Leyi Wei, Xiangrong Liu, Tzong-Yi Lee, Ying-Chih Chiang, Junwen Wang, Lantian Yao
2025 C conf
EL-DRP: An Evolutionary Learning-Based Multi-Omics Framework for Drug Response Prediction with Interpretable Biomarker Selection.
CIBCB
Yann-Jen Ho, Paik You Sheng, Yu-Ruo Chen, Yun Tang, Shinn-Ying Ho, Tzong-Yi Lee
2025 C conf
Explainable AI-Enhanced Kinase Activity Profiling Through Phosphoproteomics.
CIBCB
Chia-Ru Chung, Ming-Feng Ho, Yun Tang, Li-Ching Wu, Justin Bo-Kai Hsu, Tzong-Yi Lee, Jorng-Tzong Horng
2025 J jnl
Graph-RPI: predicting RNA-protein interactions via graph autoencoder and self-supervised learning strategies.
Briefings Bioinform.
Jiahui Guan, Lantian Yao, Peilin Xie, Zhihao Zhao, Dian Meng, Tzong-Yi Lee, Junwen Wang, Ying-Chih Chiang
2025 C conf
Integrative Multi-Omics Prognostic Modeling of Glioma Recurrence Using Variational Autoencoder and Similarity Network Fusion.
CIBCB
Phuong Lam Tran, Yun Tang, Justin Bo-Kai Hsu, Tzong-Yi Lee
2025 J jnl
STForte: tissue context-specific encoding and consistency-aware spatial imputation for spatially resolved transcriptomics.
Briefings Bioinform.
Yuxuan Pang, Chunxuan Wang, Yao-Zhong Zhang, Zhuo Wang, Seiya Imoto, Tzong-Yi Lee
2025 C conf
Self-Attention Enhanced Deep Learning Models for Immune Cell Deconvolution from Bulk RNA-Seq.
CIBCB
Chia-Ru Chung, Yen-Lin Chen, Yun Tang, Justin Bo-Kai Hsu, Li-Ching Wu, Tzong-Yi Lee, Jorng-Tzong Horng
2025 J jnl
StackDILI: Enhancing Drug-Induced Liver Injury Prediction through Stacking Strategy with Effective Molecular Representations.
J. Chem. Inf. Model.
Jiahui Guan, Danhong Dong, Peilin Xie, Zhihao Zhao, Yilin Guo, Tzong-Yi Lee, Lantian Yao, Ying-Chih Chiang
2025 J jnl
StackPIP: An Effective Computational Framework for Accurate and Balanced Identification of Proinflammatory Peptides.
J. Chem. Inf. Model.
Lantian Yao, Feng Wang, Peilin Xie, Jiahui Guan, Zhihao Zhao, Xuxin He, Xingchen Liu, Ying-Chih Chiang, Tzong-Yi Lee
2025 J jnl
Toward high-efficiency, low-resource, and explainable neuropeptide prediction with MSKDNP.
Briefings Bioinform.
Peilin Xie, Jiahui Guan, Zhihao Zhao, Yulan Liu, Zhang Cheng, Xuxin He, Xingchen Liu, Yun Tang, Zhenglong Sun, Tzong-Yi Lee, Lantian Yao, Ying-Chih Chiang
2025 C conf
Towards Accurate Identification of Anti-Hepatitis C Peptides Using Stack-AHCP.
CIBCB
Lantian Yao, Chang Liu, Yen-Peng Chiu, Jiahui Guan, Peilin Xie, Zhihao Zhao, Xingchen Liu, Yilin Guo, Yulan Liu, Yunlu Peng, Ying-Chih Chiang, Tzong-Yi Lee
2025 C conf
miSAM: Robust MicroRNA Expression Estimation Using Bi-Objective Evolutionary Learning Algorithm in Cancer Transcriptomics.
CIBCB
Yann-Lin Ho, Yann-Jen Ho, Shinn-Ying Ho, Tzong-Yi Lee
2024 J jnl
A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy.
Briefings Bioinform.
Jiahui Guan, Lantian Yao, Peilin Xie, Chia-Ru Chung, Yixian Huang, Ying-Chih Chiang, Tzong-Yi Lee
2024 J jnl
ACP-CapsPred: an explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network.
Briefings Bioinform.
Lantian Yao, Peilin Xie, Jiahui Guan, Chia-Ru Chung, Wenyang Zhang, Junyang Deng, Yixian Huang, Ying-Chih Chiang, Tzong-Yi Lee
2024 J jnl
CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network.
J. Chem. Inf. Model.
Lantian Yao, Peilin Xie, Jiahui Guan, Chia-Ru Chung, Yixian Huang, Yuxuan Pang, Huacong Wu, Ying-Chih Chiang, Tzong-Yi Lee
2024 J jnl
Guided diffusion for molecular generation with interaction prompt.
Briefings Bioinform.
Peng Wu, Huabin Du, Yingchao Yan, Tzong-Yi Lee, Chen Bai, Song Wu
2023 J jnl
A risk assessment framework for multidrug-resistant
Briefings Bioinform.
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 J jnl
Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach.
Briefings Bioinform.
Mengqi Luo, Shangfu Li, Yuxuan Pang, Lantian Yao, Renfei Ma, Hsi-Yuan Huang, Hsien-Da Huang, Tzong-Yi Lee
2023 J jnl
Holistic similarity-based prediction of phosphorylation sites for understudied kinases.
Briefings Bioinform.
Renfei Ma, Shangfu Li, Luca Parisi, Wenshuo Li, Hsien-Da Huang, Tzong-Yi Lee
2023 J jnl
Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences.
Briefings Bioinform.
Rulan Wang, Chia-Ru Chung, Hsien-Da Huang, Tzong-Yi Lee
2023 J jnl
KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites.
Genom. Proteom. Bioinform.
Renfei Ma, Shangfu Li, Wenshuo Li, Lantian Yao, Hsien-Da Huang, Tzong-Yi Lee
2023 J jnl
Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning.
J. Chem. Inf. Model.
Jiahui Guan, Lantian Yao, Chia-Ru Chung, Peilin Xie, Yilun Zhang, Junyang Deng, Ying-Chih Chiang, Tzong-Yi Lee
2022 J jnl
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers.
Nucleic Acids Res.
Yigang Chen, Lantian Yao, Yun Tang, Jhih-Hua Jhong, Jingting Wan, Jingyue Chang, Shi-Dong Cui, Yijun Luo, Xiao-Xuan Cai, Wenshuo Li, Qi Chen, Hsi-Yuan Huang, Zhuo Wang, Weiming Chen, Tzu-Hao Chang, Feng-Xiang Wei, Tzong-Yi Lee, Hsien-Da Huang
2022 J jnl
Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities.
Bioinform.
Yuxuan Pang, Lantian Yao, Jingyi Xu, Zhuo Wang, Tzong-Yi Lee
2022 J jnl
On the force field optimisation of β-lactam cores using the force field Toolkit.
J. Comput. Aided Mol. Des.
Qiyang Wu, Tianyang Huang, Songyan Xia, Frank Otto, Tzong-Yi Lee, Hsien-Da Huang, Ying-Chih Chiang
2022 J jnl
dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data.
Nucleic Acids Res.
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 J jnl
dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications.
Nucleic Acids Res.
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
2022 J jnl
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions.
Nucleic Acids Res.
Hsi-Yuan Huang, Yang-Chi-Dung Lin, Shi-Dong Cui, Yixian Huang, Yun Tang, Jia-Tong Xu, Jiayang Bao, Yulin Li, Jia Wen, Hua-Li Zuo, Weijuan Wang, Jing Li, Jie Ni, Yini Ruan, Liping Li, Yidan Chen, Yue-Yang Xie, Zihao Zhu, Xiao-Xuan Cai, Xin-Yi 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, Feng-Xiang Wei, Tzong-Yi Lee, Hsien-Da Huang
2021 J jnl
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 Bioinform.
Hsin-Yao Wang, Chia-Ru Chung, Zhuo Wang, Shangfu Li, Bo-Yu Chu, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee
2021 J jnl
A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction.
BMC Bioinform.
Mengqi Luo, Zhongyan Li, Shangfu Li, Tzong-Yi Lee
2021 J jnl
AVPIden: a new scheme for identification and functional prediction of antiviral peptides based on machine learning approaches.
Briefings Bioinform.
Yuxuan Pang, Lantian Yao, Jhih-Hua Jhong, Zhuo Wang, Tzong-Yi Lee
2021 J jnl
Identifying anti-coronavirus peptides by incorporating different negative datasets and imbalanced learning strategies.
Briefings Bioinform.
Yuxuan Pang, Zhuo Wang, Jhih-Hua Jhong, Tzong-Yi Lee
2021 J jnl
Incorporating support vector machine with sequential minimal optimization to identify anticancer peptides.
BMC Bioinform.
Yu Wan, Zhuo Wang, Tzong-Yi Lee
2021 J jnl
Large-scale mass spectrometry data combined with demographics analysis rapidly predicts methicillin resistance in
Briefings Bioinform.
Zhuo Wang, Hsin-Yao Wang, Chia-Ru Chung, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee
2021 J jnl
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions.
Database J. Biol. Databases Curation
Zhongyan Li, Siyu Chen, Jhih-Hua Jhong, Yuxuan Pang, Kai-Yao Huang, Shangfu Li, Tzong-Yi Lee
2020 J jnl
Characterization and identification of antimicrobial peptides with different functional activities.
Briefings Bioinform.
Chia-Ru Chung, Ting-Rung Kuo, Li-Ching Wu, Tzong-Yi Lee, Jorng-Tzong Horng
2020 J jnl
Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication.
Comput. Biol. Chem.
Tzong-Yi Lee, Kai-Yao Huang, Cheng-Hsiang Chuang, Cheng-Yang Lee, Tzu-Hao Chang
2020 J jnl
SuccSite: Incorporating Amino Acid Composition and Informative
Genom. Proteom. Bioinform.
Hui-Ju Kao, Van-Nui Nguyen, Kai-Yao Huang, Wen-Chi Chang, Tzong-Yi Lee
2020 J jnl
miRTarBase 2020: updates to the experimentally validated microRNA?target interaction database.
Nucleic Acids Res.
Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li, Kai-Yao Huang, Sirjana Shrestha, Hsiao-Chin Hong, Yun Tang, Yigang 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
2019 J jnl
Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites.
BMC Bioinform.
Kai-Yao Huang, Hui-Ju Kao, Justin Bo-Kai Hsu, Shun-Long Weng, Tzong-Yi Lee
2019 J jnl
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants.
Nucleic Acids Res.
Chi-Nga Chow, Tzong-Yi Lee, Yu-Cheng Hung, Guan-Zhen Li, Kuan-Chieh Tseng, Ya-Hsin Liu, Po-Li Kuo, Han-Qin Zheng, Wen-Chi Chang
2019 J jnl
Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques.
BMC Bioinform.
Hsin-Yao Wang, Wen-Chi Li, Kai-Yao Huang, Chia-Ru Chung, Jorng-Tzong Horng, Jen-Fu Hsu, Jang-Jih Lu, Tzong-Yi Lee
2019 J jnl
dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data.
Nucleic Acids Res.
Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Tsai-Hsuan Lin, Kai-Yao Huang, Tzong-Yi Lee
2019 J jnl
dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.
Nucleic Acids Res.
Kai-Yao Huang, Tzong-Yi Lee, Hui-Ju Kao, Chen-Tse Ma, Chao-Chun Lee, Tsai-Hsuan Lin, Wen-Chi Chang, Hsien-Da Huang
2018 J jnl
Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli.
BMC Genom.
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, Wen-Chi Chang
2018 J jnl
Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes.
Briefings Bioinform.
Shun-Long Weng, Kai-Yao Huang, Julia Tzu-Ya Weng, Fang-Yu Hung, Tzu-Hao Chang, Tzong-Yi Lee
2018 J jnl
Machine Learning-Based Method for Obesity Risk Evaluation Using Single-Nucleotide Polymorphisms Derived from Next-Generation Sequencing.
J. Comput. Biol.
Hsin-Yao Wang, Shih-Cheng Chang, Wan-Ying Lin, Chun-Hsien Chen, Szu-Hsien Chiang, Kai-Yao Huang, Bo-Yu Chu, Jang-Jih Lu, Tzong-Yi Lee
2017 J jnl
A New Scheme to Characterize and Identify Protein Ubiquitination Sites.
IEEE ACM Trans. Comput. Biol. Bioinform.
Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, K. Robert Lai, Tzong-Yi Lee
2017 J jnl
Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas.
BMC Syst. Biol.
Kai-Yao Huang, Tzu-Hao Chang, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K. Robert Lai, Tzong-Yi Lee
2017 J jnl
Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions.
BMC Syst. Biol.
Min-Gang Su, Julia Tzu-Ya Weng, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi, Tzong-Yi Lee
2017 J jnl
Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features.
BMC Bioinform.
Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Chien-Hsun Huang, Hui-Ju Kao, Tzu-Hao Chang, Hsin-Yao Wang, Jang-Jih Lu, Tzong-Yi Lee
2017 J jnl
MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs.
BMC Syst. Biol.
Hui-Ju Kao, Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Justin Bo-Kai Hsu, Chien-Hsun Huang, Tzong-Yi Lee
2016 J jnl
A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases.
BMC Syst. Biol.
Kai-Yao Huang, Julia Tzu-Ya Weng, Tzong-Yi Lee, Shun-Long Weng
2016 J jnl
Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis.
BMC Bioinform.
Shih-Wei Lee, Lawrence Shih-Hsin Wu, Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, Julia Tzu-Ya Weng
2016 J jnl
MDD-SOH: exploiting maximal dependence decomposition to identify
Bioinform.
Van-Minh Bui, Cheng-Tsung Lu, Trang-Thi Ho, Tzong-Yi Lee
2016 J jnl
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants.
Nucleic Acids Res.
Chi-Nga Chow, Han-Qin Zheng, Nai-Yun Wu, Chia-Hung Chien, Hsien-Da Huang, Tzong-Yi Lee, Yi-Fan Chiang-Hsieh, Ping-Fu Hou, Tien-Yi Yang, Wen-Chi Chang
2016 J jnl
SOHSite: incorporating evolutionary information and physicochemical properties to identify protein
BMC Genom.
Van-Minh Bui, Shun-Long Weng, Cheng-Tsung Lu, Tzu-Hao Chang, Julia Tzu-Ya Weng, Tzong-Yi Lee
2016 J jnl
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation.
Database J. Biol. Databases Curation
Van-Nui Nguyen, Kai-Yao Huang, Julia Tzu-Ya Weng, K. Robert Lai, Tzong-Yi Lee
2016 J jnl
UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines.
BMC Syst. Biol.
Chien-Hsun Huang, Min-Gang Su, Hui-Ju Kao, Jhih-Hua Jhong, Shun-Long Weng, Tzong-Yi Lee
2016 J jnl
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.
Nucleic Acids Res.
Kai-Yao Huang, Min-Gang Su, Hui-Ju Kao, Yun-Chung Hsieh, Jhih-Hua Jhong, Kuang-Hao Cheng, Hsien-Da Huang, Tzong-Yi Lee
2015 J jnl
A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs.
BMC Bioinform.
Hui-Ju Kao, Chien-Hsun Huang, Neil Arvin Bretaña, Cheng-Tsung Lu, Kai-Yao Huang, Shun-Long Weng, Tzong-Yi Lee
2015 J jnl
An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients.
BMC Bioinform.
Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, Julia Weng
2015 J jnl
Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities.
BMC Bioinform.
Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, Tzu-Hao Chang, Neil Arvin Bretaña, K. Robert Lai, Julia Weng, Tzong-Yi Lee
2015 J jnl
ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors.
BMC Bioinform.
Kai-Yao Huang, Tzong-Yi Lee, Yu-Chuan Teng, Tzu-Hao Chang
2015 J jnl
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein
Nucleic Acids Res.
Yi-Ju Chen, Cheng-Tsung Lu, Min-Gang Su, Kai-Yao Huang, Wei-Chieh Ching, Hsiao-Hsiang Yang, Yen-Chen Liao, Yu-Ju Chen, Tzong-Yi Lee
2014 J jnl
Characterization and identification of protein O-GlcNAcylation sites with substrate specificity.
BMC Bioinform.
Hsin-Yi Wu, Cheng-Tsung Lu, Hui-Ju Kao, Yi-Ju Chen, Yu-Ju Chen, Tzong-Yi Lee
2014 J jnl
Identification and characterization of lysine-methylated sites on histones and non-histone proteins.
Comput. Biol. Chem.
Tzong-Yi Lee, Cheng-Wei Chang, Cheng-Tsung Lu, Tzu-Hsiu Cheng, Tzu-Hao Chang
2014 J jnl
Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles.
J. Comput. Aided Mol. Des.
Justin Bo-Kai Hsu, Kai-Yao Huang, Julia Tzu-Ya Weng, Chien-Hsun Huang, Tzong-Yi Lee
2014 J jnl
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.
Database J. Biol. Databases Curation
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, Yu-Ju Chen
2014 J jnl
dbGSH: a database of
Bioinform.
Yi-Ju Chen, Cheng-Tsung Lu, Tzong-Yi Lee, Yu-Ju Chen
2014 J jnl
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins.
Nucleic Acids Res.
Min-Gang Su, Kai-Yao Huang, Cheng-Tsung Lu, Hui-Ju Kao, Ya-Han Chang, Tzong-Yi Lee
2013 J jnl
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.
J. Comput. Aided Mol. Des.
Tzu-Hao Chang, Li-Ching Wu, Tzong-Yi Lee, Shu-Pin Chen, Hsien-Da Huang, Jorng-Tzong Horng
2013 J jnl
Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures.
BMC Bioinform.
Min-Gang Su, Tzong-Yi Lee
2013 J jnl
ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins.
BMC Bioinform.
Kai-Yao Huang, Cheng-Tsung Lu, Neil Arvin Bretaña, Tzong-Yi Lee, Tzu-Hao Chang
2013 J jnl
dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.
Nucleic Acids Res.
Cheng-Tsung Lu, Kai-Yao Huang, Min-Gang Su, Tzong-Yi Lee, Neil Arvin Bretaña, Wen-Chi Chang, Yi-Ju Chen, Yu-Ju Chen, Hsien-Da Huang
2012 J jnl
GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group.
BMC Genom.
Tzong-Yi Lee, Wen-Chi Chang, Justin Bo-Kai Hsu, Tzu-Hao Chang, Dray-Ming Shien
2012 J jnl
dbSNO: a database of cysteine
Bioinform.
Tzong-Yi Lee, Yi-Ju Chen, Cheng-Tsung Lu, Wei-Chieh Ching, Yu-Chuan Teng, Hsien-Da Huang, Yu-Ju Chen
2011 J jnl
Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites.
J. Comput. Aided Mol. Des.
Cheng-Tsung Lu, Shu-An Chen, Neil Arvin Bretaña, Tzu-Hsiu Cheng, Tzong-Yi Lee
2011 J jnl
Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences.
Bioinform.
Tzong-Yi Lee, Zong-Qing Lin, Sheng-Jen Hsieh, Neil Arvin Bretaña, Cheng-Tsung Lu
2011 J jnl
Investigation and identification of protein γ-glutamyl carboxylation sites.
BMC Bioinform.
Tzong-Yi Lee, Cheng-Tsung Lu, Shu-An Chen, Neil Arvin Bretaña, Tzu-Hsiu Cheng, Min-Gang Su, Kai-Yao Huang
2011 J jnl
PlantPhos: using Maximal Dependence Decomposition to Identify Plant Phosphorylation Sites with Substrate Site Specificity.
BMC Bioinform.
Tzong-Yi Lee, Neil Arvin Bretaña, Cheng-Tsung Lu
2011 J jnl
Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties.
Bioinform.
Shu-An Chen, Yu-Yen Ou, Tzong-Yi Lee, M. Michael Gromiha
2011 J jnl
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans.
Nucleic Acids Res.
Tzong-Yi Lee, Justin Bo-Kai Hsu, Wen-Chi Chang, Hsien-Da Huang
2011 J jnl
miRTar: an integrated system for identifying miRNA-target interactions in Human.
BMC Bioinform.
Justin Bo-Kai Hsu, Chih-Min Chiu, Sheng-Da Hsu, Wei-Yun Huang, Chia-Hung Chien, Tzong-Yi Lee, Hsien-Da Huang
2010 J jnl
Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins.
BMC Bioinform.
Shu-An Chen, Tzong-Yi Lee, Yu-Yen Ou
2010 J jnl
N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites.
J. Comput. Chem.
Tzong-Yi Lee, Justin Bo-Kai Hsu, Feng-Mao Lin, Wen-Chi Chang, Po-Chiang Hsu, Hsien-Da Huang
2009 J jnl
Incorporating structural characteristics for identification of protein methylation sites.
J. Comput. Chem.
Dray-Ming Shien, Tzong-Yi Lee, Wen-Chi Chang, Justin Bo-Kai Hsu, Jorng-Tzong Horng, Po-Chiang Hsu, Ting-Yuan Wang, Hsien-Da Huang
2009 J jnl
Incorporating support vector machine for identifying protein tyrosine sulfation sites.
J. Comput. Chem.
Wen-Chi Chang, Tzong-Yi Lee, Dray-Ming Shien, Justin Bo-Kai Hsu, Jorng-Tzong Horng, Po-Chiang Hsu, Ting-Yuan Wang, Hsien-Da Huang, Rong-Long Pan
2007 J jnl
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.
Nucleic Acids Res.
Yung-Hao Wong, Tzong-Yi Lee, Han-Kuen Liang, Chia-Mao Huang, Ting-Yuan Wang, Yi-Huan Yang, Chia-Huei Chu, Hsien-Da Huang, Ming-Tat Ko, Jenn-Kang Hwang
2006 J jnl
An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints.
J. Comput. Chem.
Tzong-Yi Lee, Jorng-Tzong Horng, Hsueh-Fen Juan, Hsien-Da Huang, Li-Cheng Wu, Meng-Feng Tsai, Hsuan-Cheng Huang
2006 J jnl
ProKware: integrated software for presenting protein structural properties in protein tertiary structures.
Nucleic Acids Res.
Jui-Hung Hung, Hsien-Da Huang, Tzong-Yi Lee
2006 J jnl
dbPTM: an information repository of protein post-translational modification.
Nucleic Acids Res.
Tzong-Yi Lee, Hsien-Da Huang, Jui-Hung Hung, Hsi-Yuan Huang, Yuh-Shyong Yang, Tzu-Hao Wang
2005 J jnl
Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites.
J. Comput. Chem.
Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, Li-Cheng Wu, Jorng-Tzong Horng, Ann-Ping Tsou, Kuan-Tsae Huang
2005 J jnl
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites.
Nucleic Acids Res.
Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, Jorng-Tzong Horng