Hsien-Da Huang

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. Journal of Computer-Aided Molecular Design 27(1): 91-103 (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 Research 41(Database-Issue): 295-305 (2013)

Tzong-Yi Lee, Yi-Ju Chen, Cheng-Tsung Lu, Wei-Chieh Ching, Yu-Chuan Teng, Hsien-Da Huang, Yu-Ju Chen: dbSNO: a database of cysteine S-nitrosylation. Bioinformatics 28(17): 2293-2295 (2012)

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. IJBRA 8(3/4): 192-209 (2012)

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 Bioinformatics 12: 300 (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. Med. Biol. Engineering and Computing 49(4): 463-472 (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 Huang, Ann-Ping Tsou, Hsien-Da Huang: miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Research 39(Database-Issue): 163-169 (2011)

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 Research 39(Database-Issue): 777-787 (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): 2202-2213 (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): 5549-5557 (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. Journal of Computational Chemistry 31(15): 2759-2771 (2010)

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 Bioinformatics 10: 328 (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): 668-674 (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): 9007-9014 (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. Journal of Computational Chemistry 30(9): 1532-1543 (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. Journal of Computational Chemistry 30(15): 2526-2537 (2009)

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 Research 37(Database-Issue): 150-154 (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 Research 37(Web-Server-Issue): 129-134 (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: 22-29

Tzu-Hao Chang, Li-Ching Wu, Chi-Ta Yeh, Cheng-Wei Chang, Baw-Jhiune Liu, Hsien-Da Huang, Jorng-Tzong Horng: RiboSW . BIBE 2009: 260-265

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 Research 36(Database-Issue): 165-169 (2008)

Tzu-Hao Chang, Jorng-Tzong Horng, Hsien-Da Huang: RNALogo: a new approach to display structural RNA alignment. Nucleic Acids Research 36(Web-Server-Issue): 91-96 (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 Transactions on Information Technology in Biomedicine 12(6): 689-695 (2008)

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 Research 35(Database-Issue): 381-385 (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 Research 35(Web-Server-Issue): 588-594 (2007)

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): 855-863 (2007)

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. Journal of Computational Chemistry 27(6): 798-808 (2006)

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. Journal of Computational Chemistry 27(9): 1020-1032 (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 Research 34(Database-Issue): 135-139 (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 Research 34(Database-Issue): 622-627 (2006)

Jui-Hung Hung, Hsien-Da Huang, Tzong-Yi Lee: ProKware: integrated software for presenting protein structural properties in protein tertiary structures. Nucleic Acids Research 34(Web-Server-Issue): 89-94 (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 Research 34(Web-Server-Issue): 423-428 (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 Research 34(Web-Server-Issue): 429-434 (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 Transactions on Information Technology in Biomedicine 10(3): 550-558 (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 Transactions on Information Technology in Biomedicine 10(4): 705-713 (2006)

Hsien-Da Huang, Jorng-Tzong Horng, Li-Cheng Wu, Shu-Fen Fang: Discovering Common Structural Motifs of Ribosomal Rna Secondary Structures in Prokaryotes. International Journal on Artificial Intelligence Tools 14(4): 621-640 (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. Journal of Computational Chemistry 26(10): 1032-1041 (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 Research 33(Database-Issue): 80-85 (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 Research 33(Web-Server-Issue): 226-229 (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: 309-318

Feng-Mao Lin, Hsien-Da Huang, Hsi-Yuan Huang, Jorng-Tzong Horng: Primer design for multiplex PCR using a genetic algorithm. GECCO 2005: 475-476

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): 1141-1159 (2004)

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 Transactions on Information Technology in Biomedicine 8(1): 59-66 (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: 325-332

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: 751-760

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: 637-642

Jorng-Tzong Horng, Hsien-Da Huang, Shih-Hsien Wang, Ming-You Chen, Shir-Ly Huang, Jenn-Kang Hwang: Computing motif correlations in proteins. Journal of Computational Chemistry 24(16): 2032-2043 (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): 923-942 (2003)

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 Transactions on Information Technology in Biomedicine 7(2): 93-100 (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: 297-304

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. In Silico Biology 2: 25 (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. Journal of Computational Biology 9(4): 621-640 (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: 104-111

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: 90-95

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: 170-173