RNAMST: efficient and flexible approach for identifying RNA structural homologs. - Tzu-Hao Chang; Hsien-Da Huang; Tzu-Neng Chuang; Dray-Ming Shien; Jorng-Tzong Horng (Nucleic Acids Res., 2006)

RNALogo: a new approach to display structural RNA alignment. - Tzu-Hao Chang; Jorng-Tzong Horng; Hsien-Da Huang (Nucleic Acids Res., 2008)

RiboSW . - Tzu-Hao Chang; Li-Ching Wu; Chi-Ta Yeh; Cheng-Wei Chang; Baw-Jhiune Liu; Hsien-Da Huang; Jorng-Tzong Horng (BIBE, 2009)

Prediction of small non-coding RNA in bacterial genomes using support vector machines. - Tzu-Hao Chang; Li-Ching Wu; Jun-Hong Lin; Hsien-Da Huang; Baw-Jhiune Liu; Kuang-Fu Cheng; Jorng-Tzong Horng (Expert Syst. Appl., 2010)

Characterization and prediction of mRNA polyadenylation sites in human genes. - Tzu-Hao Chang; Li-Ching Wu; Yu-Ting Chen; Hsien-Da Huang; Baw-Jhiune Liu; Kuang-Fu Cheng; Jorng-Tzong Horng (Medical Biol. Eng. Comput., 2011)

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)

Identifying cancer highly-expressed membrane receptors for targeted drug delivery. - Wei-Chih Huang; Feng-Mao Lin; Tzu-Hao Chang; Kuang-Wen Liao; Hsien-Da Huang (Int. J. Bioinform. Res. Appl., 2012)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Benzodiazepines use and breast cancer risk: A population-based study and gene expression profiling evidence. - Usman Iqbal; Tzu-Hao Chang; Phung Anh Nguyen; Syed Abdul Shabbir; Hsuan-Chia Yang; Chih-Wei Huang; Suleman Atique; Wei-Chung Yang; Max Moldovan; Wen-Shan Jian; Min-Huei Hsu; Yun Yen; et al. (J. Biomed. Informatics, 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)

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)

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)

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)

Concatenated Channel Coding with Ring Structure in Screen-Camera Links. - Tzu-Hao Chang; Hsu-Feng Hsiao (ICAIIC, 2025)