Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites. - Hsien-Da Huang; Tzong-Yi Lee; Shih-Wei Tzeng; Li-Cheng Wu; Jorng-Tzong Horng; Ann-Ping Tsou; Kuan-Tsae Huang (J. Comput. Chem., 2005)

KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. - Hsien-Da Huang; Tzong-Yi Lee; Shih-Wei Tzeng; Jorng-Tzong Horng (Nucleic Acids Res., 2005)

An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints. - Tzong-Yi Lee; Jorng-Tzong Horng; Hsueh-Fen Juan; Hsien-Da Huang; Li-Cheng Wu; Meng-Feng Tsai; Hsuan-Cheng Huang (J. Comput. Chem., 2006)

ProKware: integrated software for presenting protein structural properties in protein tertiary structures. - Jui-Hung Hung; Hsien-Da Huang; Tzong-Yi Lee (Nucleic Acids Res., 2006)

dbPTM: an information repository of protein post-translational modification. - Tzong-Yi Lee; Hsien-Da Huang; Jui-Hung Hung; Hsi-Yuan Huang; Yuh-Shyong Yang; Tzu-Hao Wang (Nucleic Acids Res., 2006)

KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. - 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 (Nucleic Acids Res., 2007)

Incorporating support vector machine for identifying protein tyrosine sulfation sites. - 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 (J. Comput. Chem., 2009)

Incorporating structural characteristics for identification of protein methylation sites. - 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 (J. Comput. Chem., 2009)

Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins. - Shu-An Chen; Tzong-Yi Lee; Yu-Yen Ou (BMC Bioinform., 2010)

N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites. - Tzong-Yi Lee; Justin Bo-Kai Hsu; Feng-Mao Lin; Wen-Chi Chang; Po-Chiang Hsu; Hsien-Da Huang (J. Comput. Chem., 2010)

Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties. - Shu-An Chen; Yu-Yen Ou; Tzong-Yi Lee; M. Michael Gromiha (Bioinform., 2011)

Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences. - Tzong-Yi Lee; Zong-Qing Lin; Sheng-Jen Hsieh; Neil Arvin Bretaña; Cheng-Tsung Lu (Bioinform., 2011)

miRTar: an integrated system for identifying miRNA-target interactions in Human. - Justin Bo-Kai Hsu; Chih-Min Chiu; Sheng-Da Hsu; Wei-Yun Huang; Chia-Hung Chien; Tzong-Yi Lee; Hsien-Da Huang (BMC Bioinform., 2011)

PlantPhos: using Maximal Dependence Decomposition to Identify Plant Phosphorylation Sites with Substrate Site Specificity. - Tzong-Yi Lee; Neil Arvin Bretaña; Cheng-Tsung Lu (BMC Bioinform., 2011)

Investigation and identification of protein γ-glutamyl carboxylation sites. - Tzong-Yi Lee; Cheng-Tsung Lu; Shu-An Chen; Neil Arvin Bretaña; Tzu-Hsiu Cheng; Min-Gang Su; Kai-Yao Huang (BMC Bioinform., 2011)

Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites. - Cheng-Tsung Lu; Shu-An Chen; Neil Arvin Bretaña; Tzu-Hsiu Cheng; Tzong-Yi Lee (J. Comput. Aided Mol. Des., 2011)

RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. - Tzong-Yi Lee; Justin Bo-Kai Hsu; Wen-Chi Chang; Hsien-Da Huang (Nucleic Acids Res., 2011)

dbSNO: a database of cysteine S-nitrosylation. - Tzong-Yi Lee; Yi-Ju Chen; Cheng-Tsung Lu; Wei-Chieh Ching; Yu-Chuan Teng; Hsien-Da Huang; Yu-Ju Chen (Bioinform., 2012)

GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. - Tzong-Yi Lee; Wen-Chi Chang; Justin Bo-Kai Hsu; Tzu-Hao Chang; Dray-Ming Shien (BMC Genom., 2012)

ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins. - Kai-Yao Huang; Cheng-Tsung Lu; Neil Arvin Bretaña; Tzong-Yi Lee; Tzu-Hao Chang (BMC Bioinform., 2013)

Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures. - Min-Gang Su; Tzong-Yi Lee (BMC Bioinform., 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. - Tzu-Hao Chang; Li-Ching Wu; Tzong-Yi Lee; Shu-Pin Chen; Hsien-Da Huang; Jorng-Tzong Horng (J. Comput. Aided Mol. Des., 2013)

dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. - 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 (Nucleic Acids Res., 2013)

RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. - 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 (Database J. Biol. Databases Curation, 2014)

dbGSH: a database of S-glutathionylation. - Yi-Ju Chen; Cheng-Tsung Lu; Tzong-Yi Lee; Yu-Ju Chen (Bioinform., 2014)

Characterization and identification of protein O-GlcNAcylation sites with substrate specificity. - Hsin-Yi Wu; Cheng-Tsung Lu; Hui-Ju Kao; Yi-Ju Chen; Yu-Ju Chen; Tzong-Yi Lee (BMC Bioinform., 2014)

Identification and characterization of lysine-methylated sites on histones and non-histone proteins. - Tzong-Yi Lee; Cheng-Wei Chang; Cheng-Tsung Lu; Tzu-Hsiu Cheng; Tzu-Hao Chang (Comput. Biol. Chem., 2014)

Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles. - Justin Bo-Kai Hsu; Kai-Yao Huang; Julia Tzu-Ya Weng; Chien-Hsun Huang; Tzong-Yi Lee (J. Comput. Aided Mol. Des., 2014)

topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins. - Min-Gang Su; Kai-Yao Huang; Cheng-Tsung Lu; Hui-Ju Kao; Ya-Han Chang; Tzong-Yi Lee (Nucleic Acids Res., 2014)

An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients. - Guan-Mau Huang; Kai-Yao Huang; Tzong-Yi Lee; Julia Weng (BMC Bioinform., 2015)

ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors. - Kai-Yao Huang; Tzong-Yi Lee; Yu-Chuan Teng; Tzu-Hao Chang (BMC Bioinform., 2015)

Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities. - Van-Nui Nguyen; Kai-Yao Huang; Chien-Hsun Huang; Tzu-Hao Chang; Neil Arvin Bretaña; K. Robert Lai; Julia Weng; Tzong-Yi Lee (BMC Bioinform., 2015)

dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. - 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 (Nucleic Acids Res., 2015)

A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs. - Hui-Ju Kao; Chien-Hsun Huang; Neil Arvin Bretaña; Cheng-Tsung Lu; Kai-Yao Huang; Shun-Long Weng; Tzong-Yi Lee (BMC Bioinform., 2015)

UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. - Van-Nui Nguyen; Kai-Yao Huang; Julia Tzu-Ya Weng; K. Robert Lai; Tzong-Yi Lee (Database J. Biol. Databases Curation, 2016)

MDD-SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs. - Van-Minh Bui; Cheng-Tsung Lu; Trang-Thi Ho; Tzong-Yi Lee (Bioinform., 2016)

Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis. - Shih-Wei Lee; Lawrence Shih-Hsin Wu; Guan-Mau Huang; Kai-Yao Huang; Tzong-Yi Lee; Julia Tzu-Ya Weng (BMC Bioinform., 2016)

SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S-sulfenylation sites. - Van-Minh Bui; Shun-Long Weng; Cheng-Tsung Lu; Tzu-Hao Chang; Julia Tzu-Ya Weng; Tzong-Yi Lee (BMC Genom., 2016)

UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines. - Chien-Hsun Huang; Min-Gang Su; Hui-Ju Kao; Jhih-Hua Jhong; Shun-Long Weng; Tzong-Yi Lee (BMC Syst. Biol., 2016)

A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. - Kai-Yao Huang; Julia Tzu-Ya Weng; Tzong-Yi Lee; Shun-Long Weng (BMC Syst. Biol., 2016)

PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. - 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 (Nucleic Acids Res., 2016)

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. - Kai-Yao Huang; Min-Gang Su; Hui-Ju Kao; Yun-Chung Hsieh; Jhih-Hua Jhong; Kuang-Hao Cheng; Hsien-Da Huang; Tzong-Yi Lee (Nucleic Acids Res., 2016)

Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features. - 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 (BMC Bioinform., 2017)

Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas. - Kai-Yao Huang; Tzu-Hao Chang; Jhih-Hua Jhong; Yu-Hsiang Chi; Wen-Chi Li; Chien-Lung Chan; K. Robert Lai; Tzong-Yi Lee (BMC Syst. Biol., 2017)

MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs. - Hui-Ju Kao; Shun-Long Weng; Kai-Yao Huang; Fergie Joanda Kaunang; Justin Bo-Kai Hsu; Chien-Hsun Huang; Tzong-Yi Lee (BMC Syst. Biol., 2017)

Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. - Min-Gang Su; Julia Tzu-Ya Weng; Justin Bo-Kai Hsu; Kai-Yao Huang; Yu-Hsiang Chi; Tzong-Yi Lee (BMC Syst. Biol., 2017)

A New Scheme to Characterize and Identify Protein Ubiquitination Sites. - Van-Nui Nguyen; Kai-Yao Huang; Chien-Hsun Huang; K. Robert Lai; Tzong-Yi Lee (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes. - Shun-Long Weng; Kai-Yao Huang; Julia Tzu-Ya Weng; Fang-Yu Hung; Tzu-Hao Chang; Tzong-Yi Lee (Briefings Bioinform., 2018)

Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli. - 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 (BMC Genom., 2018)

Machine Learning-Based Method for Obesity Risk Evaluation Using Single-Nucleotide Polymorphisms Derived from Next-Generation Sequencing. - 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 (J. Comput. Biol., 2018)

Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites. - Kai-Yao Huang; Hui-Ju Kao; Justin Bo-Kai Hsu; Shun-Long Weng; Tzong-Yi Lee (BMC Bioinform., 2019)

PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. - 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 (Nucleic Acids Res., 2019)

dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications. - Kai-Yao Huang; Tzong-Yi Lee; Hui-Ju Kao; Chen-Tse Ma; Chao-Chun Lee; Tsai-Hsuan Lin; Wen-Chi Chang; Hsien-Da Huang (Nucleic Acids Res., 2019)

dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data. - Jhih-Hua Jhong; Yu-Hsiang Chi; Wen-Chi Li; Tsai-Hsuan Lin; Kai-Yao Huang; Tzong-Yi Lee (Nucleic Acids Res., 2019)

Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques. - Hsin-Yao Wang; Wen-Chi Li; Kai-Yao Huang; Chia-Ru Chung; Jorng-Tzong Horng; Jen-Fu Hsu; Jang-Jih Lu; Tzong-Yi Lee (BMC Bioinform., 2019)

Characterization and identification of antimicrobial peptides with different functional activities. - Chia-Ru Chung; Ting-Rung Kuo; Li-Ching Wu; Tzong-Yi Lee; Jorng-Tzong Horng (Briefings Bioinform., 2020)

Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication. - Tzong-Yi Lee; Kai-Yao Huang; Cheng-Hsiang Chuang; Cheng-Yang Lee; Tzu-Hao Chang (Comput. Biol. Chem., 2020)

SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites. - Hui-Ju Kao; Van-Nui Nguyen; Kai-Yao Huang; Wen-Chi Chang; Tzong-Yi Lee (Genom. Proteom. Bioinform., 2020)

miRTarBase 2020: updates to the experimentally validated microRNA?target interaction database. - Hsi-Yuan Huang; Yang-Chi-Dung Lin; Jing Li; Kai-Yao Huang; Sirjana Shrestha; Hsiao-Chin Hong; Yun Tang; Yigang Chen 001; Chen-Nan Jin; Yuan Yu; Jia-Tong Xu; Yue-Ming Li; et al. (Nucleic Acids Res., 2020)

Identifying anti-coronavirus peptides by incorporating different negative datasets and imbalanced learning strategies. - Yuxuan Pang; Zhuo Wang; Jhih-Hua Jhong; Tzong-Yi Lee (Briefings Bioinform., 2021)

AVPIden: a new scheme for identification and functional prediction of antiviral peptides based on machine learning approaches. - Yuxuan Pang; Lantian Yao; Jhih-Hua Jhong; Zhuo Wang; Tzong-Yi Lee (Briefings Bioinform., 2021)

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. - Hsin-Yao Wang; Chia-Ru Chung; Zhuo Wang; Shangfu Li; Bo-Yu Chu; Jorng-Tzong Horng; Jang-Jih Lu; Tzong-Yi Lee (Briefings Bioinform., 2021)

UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions. - Zhongyan Li; Siyu Chen; Jhih-Hua Jhong; Yuxuan Pang; Kai-Yao Huang; Shangfu Li; Tzong-Yi Lee (Database J. Biol. Databases Curation, 2021)

A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction. - Mengqi Luo; Zhongyan Li; Shangfu Li; Tzong-Yi Lee (BMC Bioinform., 2021)

Incorporating support vector machine with sequential minimal optimization to identify anticancer peptides. - Yu Wan; Zhuo Wang; Tzong-Yi Lee (BMC Bioinform., 2021)

On the force field optimisation of β-lactam cores using the force field Toolkit. - Qiyang Wu; Tianyang Huang; Songyan Xia; Frank Otto; Tzong-Yi Lee; Hsien-Da Huang; Ying-Chih Chiang (J. Comput. Aided Mol. Des., 2022)

CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers. - Yigang Chen 001; 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; et al. (Nucleic Acids Res., 2022)

miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. - 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; et al. (Nucleic Acids Res., 2022)

dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data. - 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; et al. (Nucleic Acids Res., 2022)

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. - 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; et al. (Nucleic Acids Res., 2022)

Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities. - Yuxuan Pang; Lantian Yao; Jingyi Xu; Zhuo Wang; Tzong-Yi Lee (Bioinform., 2022)

KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites. - Renfei Ma; Shangfu Li; Wenshuo Li; Lantian Yao; Hsien-Da Huang; Tzong-Yi Lee (Genom. Proteom. Bioinform., 2023)

Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach. - Mengqi Luo; Shangfu Li; Yuxuan Pang; Lantian Yao; Renfei Ma; Hsi-Yuan Huang; Hsien-Da Huang; Tzong-Yi Lee (Briefings Bioinform., 2023)

Holistic similarity-based prediction of phosphorylation sites for understudied kinases. - Renfei Ma; Shangfu Li; Luca Parisi; Wenshuo Li; Hsien-Da Huang; Tzong-Yi Lee (Briefings Bioinform., 2023)

Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences. - Rulan Wang; Chia-Ru Chung; Hsien-Da Huang; Tzong-Yi Lee (Briefings Bioinform., 2023)

A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology. - Zhuo Wang; Yuxuan Pang; Chia-Ru Chung; Hsin-Yao Wang; Haiyan Cui; Ying-Chih Chiang; Jorng-Tzong Horng; Jang-Jih Lu; Tzong-Yi Lee (Briefings Bioinform., 2023)

Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning. - Jiahui Guan; Lantian Yao; Chia-Ru Chung; Peilin Xie; Yilun Zhang; Junyang Deng; Ying-Chih Chiang; Tzong-Yi Lee (J. Chem. Inf. Model., 2023)

A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy. - Jiahui Guan; Lantian Yao; Peilin Xie; Chia-Ru Chung; Yixian Huang; Ying-Chih Chiang; Tzong-Yi Lee (Briefings Bioinform., 2024)

STForte: tissue context-specific encoding and consistency-aware spatial imputation for spatially resolved transcriptomics. - Yuxuan Pang; Chunxuan Wang; Yao-zhong Zhang; Zhuo Wang; Seiya Imoto; Tzong-Yi Lee (Briefings Bioinform., 2024)

Guided diffusion for molecular generation with interaction prompt. - Peng Wu; Huabin Du; Yingchao Yan; Tzong-Yi Lee; Chen Bai; Song Wu (Briefings Bioinform., 2024)

ACP-CapsPred: an explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network. - Lantian Yao; Peilin Xie; Jiahui Guan; Chia-Ru Chung; Wenyang Zhang; Junyang Deng; Yixian Huang; Ying-Chih Chiang; Tzong-Yi Lee (Briefings Bioinform., 2024)

CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network. - Lantian Yao; Peilin Xie; Jiahui Guan; Chia-Ru Chung; Yixian Huang; Yuxuan Pang; Huacong Wu; Ying-Chih Chiang; Tzong-Yi Lee (J. Chem. Inf. Model., 2024)

Graph-RPI: predicting RNA-protein interactions via graph autoencoder and self-supervised learning strategies. - Jiahui Guan; Lantian Yao; Peilin Xie; Zhihao Zhao; Dian Meng; Tzong-Yi Lee; Junwen Wang; Ying-Chih Chiang (Briefings Bioinform., 2025)

StackDILI: Enhancing Drug-Induced Liver Injury Prediction through Stacking Strategy with Effective Molecular Representations. - Jiahui Guan; Danhong Dong; Peilin Xie; Zhihao Zhao; Yilin Guo; Tzong-Yi Lee; Lantian Yao; Ying-Chih Chiang (J. Chem. Inf. Model., 2025)

StackPIP: An Effective Computational Framework for Accurate and Balanced Identification of Proinflammatory Peptides. - Lantian Yao; Feng Wang; Peilin Xie; Jiahui Guan; Zhihao Zhao; Xuxin He; Xingchen Liu; Ying-Chih Chiang; Tzong-Yi Lee (J. Chem. Inf. Model., 2025)