Hsien-Da Huang

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 27

Top Topics

Machine Learning

Regulatory Networks

Experimentally Validated

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Comput. Biol. Chem.

Publications

Yixian Huang, Danhong Dong, Wenyang Zhang, Ruiting Wang, Yang-Chi-Dung Lin, Hua-Li Zuo, Hsi-Yuan Huang, Hsien-Da Huang
DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning. Database J. Biol. Databases Curation 2024 (2024)
Renfei Ma, Shangfu Li, Wenshuo Li, Lantian Yao, Hsien-Da Huang, Tzong-Yi Lee
KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites. Genom. Proteom. Bioinform. 21 (1) (2023)
Yi-Gang Chen, Yang-Chi-Dung Lin, Yijun Luo, Xiao-Xuan Cai, Peng Qiu, Shi-Dong Cui, Zhe Wang, Hsi-Yuan Huang, Hsien-Da Huang
Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis. Briefings Bioinform. 24 (3) (2023)
Renfei Ma, Shangfu Li, Luca Parisi, Wenshuo Li, Hsien-Da Huang, Tzong-Yi Lee
Holistic similarity-based prediction of phosphorylation sites for understudied kinases. Briefings Bioinform. 24 (2) (2023)
Rulan Wang, Chia-Ru Chung, Hsien-Da Huang, Tzong-Yi Lee
Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences. Briefings Bioinform. 24 (2) (2023)
Mengqi Luo, Shangfu Li, Yuxuan Pang, Lantian Yao, Renfei Ma, Hsi-Yuan Huang, Hsien-Da Huang, Tzong-Yi Lee
Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach. Briefings Bioinform. 24 (1) (2023)
Yi-Gang 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
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers. Nucleic Acids Res. 50 (D1) (2022)
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
dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. Nucleic Acids Res. 50 (D1) (2022)
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, Yi-Gang 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
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. Nucleic Acids Res. 50 (D1) (2022)
Qiyang Wu, Tianyang Huang, Songyan Xia, Frank Otto, Tzong-Yi Lee, Hsien-Da Huang, Ying-Chih Chiang
On the force field optimisation of β-lactam cores using the force field Toolkit. J. Comput. Aided Mol. Des. 36 (7) (2022)
Hsi-Yuan Huang, Jing Li, Yun Tang, Yi-Xian Huang, Yi-Gang Chen, Yue-Yang Xie, Zhe-Yuan Zhou, Xin-Yi Chen, Si-Yuan Ding, Meng-Fan Luo, Chen-Nan Jin, Le-Shan Zhao, Jia-Tong Xu, Ying Zhou, Yang-Chi-Dung Lin, Hsiao-Chin Hong, Hua-Li Zuo, Si-Yao Hu, Pei-Yi Xu, Xin Li, Hsien-Da Huang
MethHC 2.0: information repository of DNA methylation and gene expression in human cancer. Nucleic Acids Res. 49 (Database-Issue) (2021)
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, Ting-Hsuan Sun, Shun-Long Weng, Ching-Ping Tseng, Hsien-Da Huang
Multi-omics profiling reveals microRNA-mediated insulin signaling networks. BMC Bioinform. (13) (2020)
Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li, Kai-Yao Huang, Sirjana Shrestha, Hsiao-Chin Hong, Yun Tang, Yi-Gang 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
miRTarBase 2020: updates to the experimentally validated microRNA?target interaction database. Nucleic Acids Res. 48 (Database-Issue) (2020)
Chengyu Liu, Yu-Chen Liu, Hsien-Da Huang, Wei Wang
Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model. Bioinform. 35 (23) (2019)
Kai-Yao Huang, Tzong-Yi Lee, Hui-Ju Kao, Chen-Tse Ma, Chao-Chun Lee, Tsai-Hsuan Lin, Wen-Chi Chang, Hsien-Da Huang
dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications. Nucleic Acids Res. 47 (Database-Issue) (2019)
Chih-Hung Chou, Sirjana Shrestha, Chi-Dung Yang, Nai-Wen Chang, Yu-Ling Lin, Kuang-Wen Liao, Wei-Chih Huang, Ting-Hsuan Sun, Siang-Jyun Tu, Wei-Hsiang Lee, Men-Yee Chiew, Chun-San Tai, Ting-Yen Wei, Tzi-Ren Tsai, Hsin-Tzu Huang, Chung-Yu Wang, Hsin-Yi Wu, Shu-Yi Ho, Pin-Rong Chen, Cheng-Hsun Chuang, Pei-Jung Hsieh, Yi-Shin Wu, Wen-Liang Chen, Meng-Ju Li, Yu-chun Wu, Xin-Yi Huang, Fung Ling Ng, Waradee Buddhakosai, Pei-Chun Huang, Kuan-Chun Lan, Chia-Yen Huang, Shun-Long Weng, Yeong-Nan Cheng, Chao Liang, Wen-Lian Hsu, Hsien-Da Huang
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic Acids Res. 46 (Database-Issue) (2018)
Chih-Hung Chou, Hsi-Yuan Huang, Wei-Chih Huang, 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
The aquatic animals' transcriptome resource for comparative functional analysis. BMC Genom. 19 (S2) (2018)
Wei-Hsiang Kung, Andy Chi-Lung Lee, Chi-Dung Yang, Ching-Fang Yu, Men-Yee Chiew, Fang-Hsin Chen, Hsien-Da Huang
Integrated microRNA and mRNA expression profile analysis of tumor-associated macrophages after exposure to single-dose irradiation. Comput. Biol. Chem. 74 (2018)
Yu-Chen Liu, Hsiao-Chin Hong, Chi-Dung Yang, Wei-Hsiang Lee, Hsin-Tzu Huang, Hsien-Da Huang
Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis. BMC Genom. 19 (S2) (2018)
Yu-Chen Liu, Wen Liang Chen, Wei-Hsiang Kung, Hsien-Da Huang
Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi. BMC Genom. 18 (S2) (2017)
Wei-Hsiang Kung, Ching-Fang Yu, Andy Chi-Lung Lee, Chi-Dung Yang, Yu-Chen Liu, Fang-Hsin Chen, Hsien-Da Huang
Gene expression profiling of tumor-associated macrophages after exposure to single-dose irradiation. Comput. Biol. Chem. 69 (2017)
Yu-Chen Liu, Sheng-Da Hsu, Chih-Hung Chou, Wei-Yun Huang, Yu-Hung Chen, Chia-Yu Liu, Guan-Jay Lyu, Shao-Zhen Huang, Sergey Aganezov Jr., Max A. Alekseyev, Chung-Der Hsiao, Hsien-Da Huang
draft genome. BMC Genom. 17 (S-1) (2016)
Kai-Yao Huang, Min-Gang Su, Hui-Ju Kao, Yun-Chung Hsieh, Jhih-Hua Jhong, Kuang-Hao Cheng, Hsien-Da Huang, Tzong-Yi Lee
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. Nucleic Acids Res. 44 (Database-Issue) (2016)
Chih-Hung Chou, Nai-Wen Chang, 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, Ting-Yan Jian, Hsin-Yi Wu, Pin-Rong Chen, Nai-Chieh Lin, Hsin-Tzu Huang, Tzu-Ling Yang, Chung-Yuan Pai, Chun-San Tai, Wen-Liang Chen, Chia-Yen Huang, Chun-Chi Liu, Shun-Long Weng, Kuang-Wen Liao, Wen-Lian Hsu, Hsien-Da Huang
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res. 44 (Database-Issue) (2016)
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
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. Nucleic Acids Res. 44 (Database-Issue) (2016)
Richie Ruei-Chi Gan, Ting-Wen Chen, Timothy H. Wu, Po-Jung Huang, Chi-Ching Lee, Yuan-Ming Yeh, Cheng-Hsun Chiu, Hsien-Da Huang, Petrus Tang
PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms. BMC Bioinform. 17 (S-19) (2016)
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
CircNet: a database of circular RNAs derived from transcriptome sequencing data. Nucleic Acids Res. 44 (Database-Issue) (2016)
Hsien-Da Huang, Yi-Ping Phoebe Chen
Editorial. Comput. Biol. Chem. 57 (2015)
Yi-Hsiung Chen, Chi-Dung Yang, Ching-Ping Tseng, Hsien-Da Huang, Shinn-Ying Ho
GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes. Bioinform. 31 (13) (2015)
Wei-Yun Huang, Sheng-Da Hsu, Hsi-Yuan Huang, Yi-Ming Sun, Chih-Hung Chou, Shun-Long Weng, Hsien-Da Huang
MethHC: a database of DNA methylation and gene expression in human cancer. Nucleic Acids Res. 43 (Database-Issue) (2015)
Hsien-Da Huang, Yi-Ping Phoebe Chen
Guest Editorial for the 13th Asia Pacific Bioinformatics Conference. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (6) (2015)
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
Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing. J. Clin. Bioinform. 4 (2014)
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
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. Database J. Biol. Databases Curation 2014 (2014)
Wen-Ling Chan, Hsien-Da Huang, Jan-Gowth Chang
lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome. Comput. Biol. Chem. 50 (2014)
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, Tzu-Hao Chang, Shun-Long Weng, Kuang-Wen Liao, I-En Liao, Chun-Chi Liu, Hsien-Da Huang
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res. 42 (Database-Issue) (2014)
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
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing. BMC Genom. 14 (S-1) (2013)
Wen-Ling Chan, Wen-Kuang Yang, Hsien-Da Huang, Jan-Gowth Chang
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes. Database J. Biol. Databases Curation 2013 (2013)
Tzu-Hao Chang, Hsi-Yuan Huang, Justin Bo-Kai Hsu, Shun-Long Weng, Jorng-Tzong Horng, Hsien-Da Huang
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinform. 14 (S-2) (2013)
Tzu-Hao Chang, Li-Ching Wu, Tzong-Yi Lee, Shu-Pin Chen, Hsien-Da Huang, Jorng-Tzong Horng
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. 27 (1) (2013)
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
dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. Nucleic Acids Res. 41 (Database-Issue) (2013)
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
Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing. IWBBIO (2013)
Wei-Chih Huang, Feng-Mao Lin, Tzu-Hao Chang, Kuang-Wen Liao, Hsien-Da Huang
Identifying cancer highly-expressed membrane receptors for targeted drug delivery. Int. J. Bioinform. Res. Appl. 8 (3/4) (2012)
Tzong-Yi Lee, Yi-Ju Chen, Cheng-Tsung Lu, Wei-Chieh Ching, Yu-Chuan Teng, Hsien-Da Huang, Yu-Ju Chen
-nitrosylation. Bioinform. 28 (17) (2012)
Tzong-Yi Lee, Justin Bo-Kai Hsu, Wen-Chi Chang, Hsien-Da Huang
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. Nucleic Acids Res. 39 (Database-Issue) (2011)
Sheng-Da Hsu, Feng-Mao Lin, Wei-Yun Wu, Chao Liang, Wei-Chih Huang, Wen-Ling Chan, Wen-Ting Tsai, Goun-Zhou Chen, Chia-Jung Lee, Chih-Min Chiu, Chia-Hung Chien, Ming-Chia Wu, Chi-Ying F. Huang, Ann-Ping Tsou, Hsien-Da Huang
miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res. 39 (Database-Issue) (2011)
Tzu-Hao Chang, Li-Ching Wu, Yu-Ting Chen, Hsien-Da Huang, Baw-Jhiune Liu, Kuang-Fu Cheng, Jorng-Tzong Horng
Characterization and prediction of mRNA polyadenylation sites in human genes. Medical Biol. Eng. Comput. 49 (4) (2011)
Justin Bo-Kai Hsu, Chih-Min Chiu, Sheng-Da Hsu, Wei-Yun Huang, Chia-Hung Chien, Tzong-Yi Lee, Hsien-Da Huang
miRTar: an integrated system for identifying miRNA-target interactions in Human. BMC Bioinform. 12 (2011)
Li-Ching Wu, Jhih-Long Huang, Jorng-Tzong Horng, Hsien-Da Huang
An expert system to identify co-regulated gene groups from time-lagged gene clusters using cell cycle expression data. Expert Syst. Appl. 37 (3) (2010)
Tzu-Hao Chang, Li-Ching Wu, Jun-Hong Lin, Hsien-Da Huang, Baw-Jhiune Liu, Kuang-Fu Cheng, Jorng-Tzong Horng
Prediction of small non-coding RNA in bacterial genomes using support vector machines. Expert Syst. Appl. 37 (8) (2010)
Tzong-Yi Lee, Justin Bo-Kai Hsu, Feng-Mao Lin, Wen-Chi Chang, Po-Chiang Hsu, Hsien-Da Huang
N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites. J. Comput. Chem. 31 (15) (2010)
Hsi-Yuan Huang, Heng-Yi Chang, Chih-Hung Chou, Ching-Ping Tseng, Shinn-Ying Ho, Chi-Dung Yang, Yih-Wei Ju, Hsien-Da Huang
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. Nucleic Acids Res. 37 (Database-Issue) (2009)
Wei-Chi Wang, Feng-Mao Lin, Wen-Chi Chang, Kuan-Yu Lin, Hsien-Da Huang, Na-Sheng Lin
miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinform. 10 (2009)
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
Incorporating structural characteristics for identification of protein methylation sites. J. Comput. Chem. 30 (9) (2009)
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
Incorporating support vector machine for identifying protein tyrosine sulfation sites. J. Comput. Chem. 30 (15) (2009)
Yi-Ming Sun, Wei-Li Liao, Hsien-Da Huang, Baw-Jhiune Liu, Cheng-Wei Chang, Jorng-Tzong Horng, Li-Ching Wu
A Human DNA Methylation Site Predictor Based on SVM. BIBE (2009)
Chih-Hung Chou, Wen-Chi Chang, Chih-Min Chiu, Chih-Chang Huang, Hsien-Da Huang
FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Tzu-Hao Chang, Li-Ching Wu, Chi-Ta Yeh, Cheng-Wei Chang, Baw-Jhiune Liu, Hsien-Da Huang, Jorng-Tzong Horng
RiboSW . BIBE (2009)
Li-Cheng Wu, Jian-Xin Lee, Hsien-Da Huang, Baw-Juine Liu, Jorng-Tzong Horng
An expert system to predict protein thermostability using decision tree. Expert Syst. Appl. 36 (5) (2009)
Li-Ching Wu, Hsien-Da Huang, Yu-Chung Chang, Ying-Chun Lee, Jorng-Tzong Horng
Detecting LTR structures in human genomic sequences using profile hidden Markov models. Expert Syst. Appl. 36 (1) (2009)
Tzu-Hao Chang, Jorng-Tzong Horng, Hsien-Da Huang
RNALogo: a new approach to display structural RNA alignment. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Li-Ching Wu, Jorng-Tzong Horng, Hsien-Da Huang, Wei-Long Chen
Identifying Discriminative Amino Acids Within the Hemagglutinin of Human Influenza A H5N1 Virus Using a Decision Tree. IEEE Trans. Inf. Technol. Biomed. 12 (6) (2008)
Sheng-Da Hsu, Chia-Huei Chu, Ann-Ping Tsou, Shu-Jen Chen, Hua-Chien Chen, Paul Wei-Che Hsu, Yung-Hao Wong, Yi-Hsuan Chen, Gian-Hung Chen, Hsien-Da Huang
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res. 36 (Database-Issue) (2008)
Li-Cheng Wu, Jorng-Tzong Horng, Hsi-Yuan Huang, Feng-Mao Lin, Hsien-Da Huang, Meng-Feng Tsai
Primer design for multiplex PCR using a genetic algorithm. Soft Comput. 11 (9) (2007)
Paul Wei-Che Hsu, Li-Zen Lin, Sheng-Da Hsu, Justin Bo-Kai Hsu, Hsien-Da Huang
ViTa: prediction of host microRNAs targets on viruses. Nucleic Acids Res. 35 (Database-Issue) (2007)
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
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Tzong-Yi Lee, Jorng-Tzong Horng, Hsueh-Fen Juan, Hsien-Da Huang, Li-Cheng Wu, Meng-Feng Tsai, Hsuan-Cheng Huang
An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints. J. Comput. Chem. 27 (9) (2006)
Li-Cheng Wu, Jorng-Tzong Horng, Shir-Ly Huang, Hsien-Da Huang, Baw-Jhiune Liu
Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures. J. Comput. Chem. 27 (6) (2006)
Paul Wei-Che Hsu, Hsien-Da Huang, Sheng-Da Hsu, Li-Zen Lin, Ann-Ping Tsou, Ching-Ping Tseng, Peter F. Stadler, Stefan Washietl, Ivo L. Hofacker
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res. 34 (Database-Issue) (2006)
Hsi-Yuan Huang, Chia-Hung Chien, Kuan-Hua Jen, Hsien-Da Huang
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Feng-Mao Lin, Hsien-Da Huang, Y.-C. Chang, Ann-Ping Tsou, P.-L. Chan, L.-C. Wu, Meng-Feng Tsai, Jorng-Tzong Horng
Database to Dynamically Aid Probe Design for Virus Identification. IEEE Trans. Inf. Technol. Biomed. 10 (4) (2006)
Jui-Hung Hung, Hsien-Da Huang, Tzong-Yi Lee
ProKware: integrated software for presenting protein structural properties in protein tertiary structures. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Tzong-Yi Lee, Hsien-Da Huang, Jui-Hung Hung, Hsi-Yuan Huang, Yuh-Shyong Yang, Tzu-Hao Wang
dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res. 34 (Database-Issue) (2006)
Tzu-Hao Chang, Hsien-Da Huang, Tzu-Neng Chuang, Dray-Ming Shien, Jorng-Tzong Horng
RNAMST: efficient and flexible approach for identifying RNA structural homologs. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Ann-Ping Tsou, Yi-Ming Sun, Chia-Lin Liu, Hsien-Da Huang, Jorng-Tzong Horng, Meng-Feng Tsai, Baw-Jhiune Liu
Biological Data Warehousing System for Identifying Transcriptional Regulatory Sites From Gene Expressions of Microarray Data. IEEE Trans. Inf. Technol. Biomed. 10 (3) (2006)
Feng-Mao Lin, Hsien-Da Huang, Hsi-Yuan Huang, Jorng-Tzong Horng
Primer design for multiplex PCR using a genetic algorithm. GECCO (2005)
Hsien-Da Huang, Jorng-Tzong Horng, Li-Cheng Wu, Shu-Fen Fang
Discovering Common Structural Motifs of Ribosomal Rna Secondary Structures in Prokaryotes. Int. J. Artif. Intell. Tools 14 (4) (2005)
Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, Li-Cheng Wu, Jorng-Tzong Horng, Ann-Ping Tsou, Kuan-Tsae Huang
Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites. J. Comput. Chem. 26 (10) (2005)
Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, Jorng-Tzong Horng
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Feng-Mao Lin, Hsien-Da Huang, Yu-Chung Chang, Pak-Leong Chan, Jorng-Tzong Horng, Ming-Tat Ko
A database to aid probe design for virus identification. APBC (2005)
Hsien-Da Huang, Jorng-Tzong Horng, Feng-Mao Lin, Yu-Chung Chang, Chen-Chia Huang
SpliceInfo: an information repository for mRNA alternative splicing in human genome. Nucleic Acids Res. 33 (Database-Issue) (2005)
Jorng-Tzong Horng, Kai-Chih Hu, Li-Cheng Wu, Hsien-Da Huang, Feng-Mao Lin, Shir-Ly Huang, Horn-Cheng Lai, Ton-Yuen Chu
Identifying the combination of genetic factors that determine susceptibility to cervical cancer. IEEE Trans. Inf. Technol. Biomed. 8 (1) (2004)
Yi-Ming Sun, Hsien-Da Huang, Jorng-Tzong Horng, Shir-Ly Huang, Ann-Ping Tsou
RgS-Miner: A Biological Data Warehousing, Analyzing and Mining System for Identifying Transcriptional Regulatory Sites in Human Genome. DEXA (2004)
Jorng-Tzong Horng, Kai-Chih Hu, Li-Cheng Wu, Hsien-Da Huang, Horn-Cheng Lai, Ton-Yuen Chu
Identifying the Combination of Genetic Factors that Determine Susceptibility to Cervical Cancer. BIBE (2004)
Hsien-Da Huang, Jorng-Tzong Horng, Yi-Ming Sun, Ann-Ping Tsou, Shir-Ly Huang
Identifying Transcriptional Regulatory Sites in the Human Genome Using an Integrated Computation. ISPAN (2004)
Hsien-Da Huang, Jorng-Tzong Horng, Chia-Hui Chang, Tsung-Shan Tsou, Jing-Yue Hong, Baw-Jhiune Liu
A Computational Approach to Discover Differential Cooperation of Regulartory Sites in Functionally Related Genes in Yeast Genome. J. Inf. Sci. Eng. 20 (6) (2004)
Jorng-Tzong Horng, Feng-Mao Lin, J. H. Lin, Hsien-Da Huang, Baw-Jhiune Liu
Database of repetitive elements in complete genomes and data mining using transcription factor binding sites. IEEE Trans. Inf. Technol. Biomed. 7 (2) (2003)
Hsien-Da Huang, Huei-Lin Chang, Tsung-Shan Tsou, Baw-Jhiune Liu, Jorng-Tzong Horng
A Data Mining Method to Predict Transcriptional Regulatory Sites Based Based on Differentially Expressed Genes in Human Genome. J. Inf. Sci. Eng. 19 (6) (2003)
Jorng-Tzong Horng, Hsien-Da Huang, Shih-Hsien Wang, Ming-You Chen, Shir-Ly Huang, Jenn-Kang Hwang
Computing motif correlations in proteins. J. Comput. Chem. 24 (16) (2003)
Hsien-Da Huang, Huei-Lin Chang, Tsung-Shan Tsou, Baw-Jhiune Liu, Cheng-Yan Kao, Jorng-Tzong Horng
A Data Mining Method to Predict Transcriptional Regulatory Sites Based on Differentially Expressed Genes in Human Genome. BIBE (2003)
Jorng-Tzong Horng, Hsien-Da Huang, Shir-Ly Huang, Ueng-Cheng Yang, Yu-Chang Chang
Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae. Silico Biol. 2 (3) (2002)
Jih Tsung Yang, Hsien-Da Huang, Jorng-Tzong Horng
Devising a cost effective baseball scheduling by evolutionary algorithms. IEEE Congress on Evolutionary Computation (2002)
Jorng-Tzong Horng, Hsien-Da Huang, Ming-Hui Jin, Li-Cheng Wu, Shir-Ly Huang
The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions. J. Comput. Biol. 9 (4) (2002)
Hsien-Da Huang, Shu-Fen Fang, Jorng-Tzong Horng, Cheng-Yan Kao
Discovering Common Structural Motifs from SSU 16 S Ribosomal RNA Secondary Structures. BIBE (2001)
Jorng-Tzong Horng, Hsien-Da Huang, Cho-Chun Huang, Cheng-Yan Kao
Mining Putative Regulatory Elements in Gene Promoter Regions. German Conference on Bioinformatics (2001)
Hsien-Da Huang, Shu-Fen Fang, Jorng-Tzong Horng
Mining Combinations of Structural Motif from SSU 16 S Ribosomal RNA Secondary Structures. German Conference on Bioinformatics (2001)