Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing. - Chih-Min Chiu; Feng-Mao Lin; Tzu-Hao Chang; Wei-Chih Huang; Chao Liang; Wei-Yun Wu; Tzu-Ling Yang; Shun-Long Weng; Hsien-Da Huang (IWBBIO, 2013)

An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. - Tzu-Hao Chang; Hsi-Yuan Huang; Justin Bo-Kai Hsu; Shun-Long Weng; Jorng-Tzong Horng; Hsien-Da Huang (BMC Bioinform., 2013)

A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. - Chih-Hung Chou; Feng-Mao Lin; Min-Te Chou; Sheng-Da Hsu; Tzu-Hao Chang; Shun-Long Weng; Sirjana Shrestha; Chiung-Chih Hsiao; Jui-Hung Hung; Hsien-Da Huang (BMC Genom., 2013)

Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing. - Chih-Min Chiu; Feng-Mao Lin; Tzu-Hao Chang; Wei-Chih Huang; Chao Liang; Ting Yang; Wei-Yun Wu; Tzu-Ling Yang; Shun-Long Weng; Hsien-Da Huang (J. Clin. Bioinform., 2014)

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. - Sheng-Da Hsu; Yu-Ting Tseng; Sirjana Shrestha; Yu-Ling Lin; Anas Khaleel; Chih-Hung Chou; Chao-Fang Chu; Hsi-Yuan Huang; Ching-Min Lin; Shu-Yi Ho; Ting-Yan Jian; Feng-Mao Lin; et al. (Nucleic Acids Res., 2014)

MethHC: a database of DNA methylation and gene expression in human cancer. - Wei-Yun Huang; Sheng-Da Hsu; Hsi-Yuan Huang; Yi-Ming Sun; Chih-Hung Chou; Shun-Long Weng; Hsien-Da Huang (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)

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)

miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. - Chih-Hung Chou; Nai-Wen Chang 001; Sirjana Shrestha; Sheng-Da Hsu; Yu-Ling Lin; Wei-Hsiang Lee; Chi-Dung Yang; Hsiao-Chin Hong; Ting-Yen Wei; Siang-Jyun Tu; Tzi-Ren Tsai; Shu-Yi Ho; et al. (Nucleic Acids Res., 2016)

CircNet: a database of circular RNAs derived from transcriptome sequencing data. - Yu-Chen Liu; Jianrong Li; Chuan-Hu Sun; Erik Andrews; Rou-Fang Chao; Feng-Mao Lin; Shun-Long Weng; Sheng-Da Hsu; Chieh-Chen Huang; Chao Cheng; Chun-Chi Liu; Hsien-Da Huang (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)

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)

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)

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. - Chih-Hung Chou; Sirjana Shrestha; Chi-Dung Yang; Nai-Wen Chang 001; Yu-Ling Lin; Kuang-Wen Liao; Wei-Chih Huang 002; Ting-Hsuan Sun; Siang-Jyun Tu; Wei-Hsiang Lee; Men-Yee Chiew; Chun-San Tai; et al. (Nucleic Acids Res., 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)

iDPGK: characterization and identification of lysine phosphoglycerylation sites based on sequence-based features. - Kai-Yao Huang; Fang-Yu Hung; Hui-Ju Kao; Hui-Hsuan Lau; Shun-Long Weng (BMC Bioinform., 2020)

Multi-omics profiling reveals microRNA-mediated insulin signaling networks. - Yang-Chi-Dung Lin; Hsi-Yuan Huang; Sirjana Shrestha; Chih-Hung Chou; Yen-Hua Chen; Chi-Ru Chen; Hsiao-Chin Hong; Jing Li; Yi-An Chang; Men-Yee Chiew; Ya-Rong Huang; Siang-Jyun Tu; et al. (BMC Bioinform., 2020)

iDVIP: identification and characterization of viral integrase inhibitory peptides. - Kai-Yao Huang; Hui-Ju Kao; Tzu-Hsiang Weng; Chia-Hung Chen; Shun-Long Weng (Briefings Bioinform., 2022)

CPNet: Covariance-Improved Prototype Network for Limited Samples Masked Face Recognition Using Few-Shot Learning. - Sendren Sheng-Dong Xu; Albertus Andrie Christian; Chien-Peng Ho; Shun-Long Weng (IEICE Trans. Fundam. Electron. Commun. Comput. Sci., 2024)