Primer design for multiplex PCR using a genetic algorithm. - Feng-Mao Lin; Hsien-Da Huang; Hsi-Yuan Huang; Jorng-Tzong Horng (GECCO, 2005)

RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. - Hsi-Yuan Huang; Chia-Hung Chien; Kuan-Hua Jen; Hsien-Da Huang (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)

Primer design for multiplex PCR using a genetic algorithm. - Li-Cheng Wu; Jorng-Tzong Horng; Hsi-Yuan Huang; Feng-Mao Lin; Hsien-Da Huang; Meng-Feng Tsai (Soft Comput., 2007)

sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. - Hsi-Yuan Huang; Heng-Yi Chang; Chih-Hung Chou; Ching-Ping Tseng; Shinn-Ying Ho; Chi-Dung Yang; Yih-Wei Ju; Hsien-Da Huang (Nucleic Acids Res., 2009)

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)

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)

Integrated analyses to reconstruct microRNA-mediated regulatory networks in mouse liver using high-throughput profiling. - Sheng-Da Hsu; Hsi-Yuan Huang; Chih-Hung Chou; Yi-Ming Sun; Ming-Ta Hsu; Ann-Ping Tsou (BMC Genom., 2015)

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)

Establish Reporting Format of Gene Related Rare-Diseases by Exome Sequencing in the Clinical Medical Laboratory. - Cheng-Mao Ho; Hsi-Yuan Huang; Chin-An Yang; Ya-Sian Chang; Chien-Yu Lin; Jan-Gowth Chang (BIBE, 2016)

An Integrative Analysis for Cancer Studies. - Hsi-Yuan Huang; Chien-Yu Lin; Chin-An Yang; Cheng-Mao Ho; Ya-Sian Chang; Jan-Gowth Chang (BIBE, 2016)

Semiconductor Supply Chain Planning With Decisions of Decoupling Point and VMI Scenario. - Mu-Chen Chen; Yu-Hsiang Hsiao; Hsi-Yuan Huang (IEEE Trans. Syst. Man Cybern. Syst., 2017)

Mutation Analysis of Second Primary Tumors in the Head and Neck Cancer by Next Generation Sequencing. - Ting-Yuan Liu; Chien-Chin Lee; Hsi-Yuan Huang; Jan-Gowth Chang (BIBE, 2018)

The aquatic animals' transcriptome resource for comparative functional analysis. - Chih-Hung Chou; Hsi-Yuan Huang; Wei-Chih Huang 002; Sheng-Da Hsu; Chung-Der Hsiao; Chia-Yu Liu; Yu-Hung Chen; Yu-Chen Liu; Wei-Yun Huang; Meng-Lin Lee; Yi-Chang Chen; Hsien-Da Huang (BMC Genom., 2018)

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)

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)

MethHC 2.0: information repository of DNA methylation and gene expression in human cancer. - Hsi-Yuan Huang; Jing Li; Yun Tang; Yixian Huang; Yigang Chen 001; Yue-Yang Xie; Zhe-Yuan Zhou; Xin-Yi Chen; Si-Yuan Ding; Meng-Fan Luo; Chen-Nan Jin; Le-Shan Zhao; et al. (Nucleic Acids Res., 2021)

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)

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)

Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis. - Yigang Chen 001; Yang-Chi-Dung Lin; Yijun Luo; Xiao-Xuan Cai; Peng Qiu; Shi-Dong Cui; Zhe Wang; Hsi-Yuan Huang; Hsien-Da Huang (Briefings Bioinform., 2023)

DeepDrugmiR: a two-stage deep learning method for inferring small molecules' regulatory effects on microRNA expression. - Yixian Huang; Huacong Wu; Ying Cai; Danhong Dong; Sicong Yu; Yigang Chen 001; Zihao Zhu; Yang-Chi-Dung Lin; Hsien-Da Huang; Hsi-Yuan Huang (BCB, 2024)

DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning. - Yixian Huang; Danhong Dong; Wenyang Zhang; Ruiting Wang; Yang-Chi-Dung Lin; Hua-Li Zuo; Hsi-Yuan Huang; Hsien-Da Huang (Database J. Biol. Databases Curation, 2024)

SCOPE-DTI: Semi-Inductive Dataset Construction and Framework Optimization for Practical Usability Enhancement in Deep Learning-Based Drug Target Interaction Prediction. - Yigang Chen 001; Xiang Ji; Ziyue Zhang; Yuming Zhou; Yang-Chi-Dung Lin; Hsi-Yuan Huang; Tao Zhang; Yi Lai; Ke Chen; Chang Su; Xingqiao Lin; Zihao Zhu; et al. (CoRR, 2025)