Hsien-Da Huang

99 papers A 1B 2C 7Journal 84Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
DeepADR: multimodal prediction of adverse drug reaction frequency by integrating early-stage drug discovery information via Kolmogorov-Arnold networks.
Briefings Bioinform.
Jingting Wan, Chenyang Jia, Danhong Dong, Yigang Chen, Yang-Chi-Dung Lin, Yisheng He, Hsi-Yuan Huang, Hsien-Da Huang
2025 C conf
Integrative Framework for Functional analysis of multiple Traditional Chinese Medicines based on transcriptome-driven systems biology and supervised learning strategy.
CIBCB
Yun Tang, Chia-Ru Chung, Hsi-Yuan Huang, Yang-Chi-Dung Lin, Hua-Li Zuo, Jing Li, Liping Li, Siyao Hu, Hsiao-Chin Hong, Fei Wang, Jinrui Bai, Hsien-Da Huang
2025 J jnl
SCOPE-DTI: Semi-Inductive Dataset Construction and Framework Optimization for Practical Usability Enhancement in Deep Learning-Based Drug Target Interaction Prediction.
CoRR
Yigang Chen, 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, Yanggyi Zhang, Kangping Wei, Jiehui Fu, Yixian Huang, Shi-Dong Cui, Shih-Chung Yen, Ariel Warshel, Hsien-Da Huang
2024 — conf
DeepDrugmiR: a two-stage deep learning method for inferring small molecules' regulatory effects on microRNA expression.
BCB
Yixian Huang, Huacong Wu, Ying Cai, Danhong Dong, Sicong Yu, Yigang Chen, Zihao Zhu, Yang-Chi-Dung Lin, Hsien-Da Huang, Hsi-Yuan Huang
2024 J jnl
DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning.
Database J. Biol. Databases Curation
Yixian Huang, Danhong Dong, Wenyang Zhang, Ruiting Wang, Yang-Chi-Dung Lin, Hua-Li Zuo, Hsi-Yuan Huang, Hsien-Da Huang
2023 J jnl
Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach.
Briefings Bioinform.
Mengqi Luo, Shangfu Li, Yuxuan Pang, Lantian Yao, Renfei Ma, Hsi-Yuan Huang, Hsien-Da Huang, Tzong-Yi Lee
2023 J jnl
Holistic similarity-based prediction of phosphorylation sites for understudied kinases.
Briefings Bioinform.
Renfei Ma, Shangfu Li, Luca Parisi, Wenshuo Li, Hsien-Da Huang, Tzong-Yi Lee
2023 J jnl
Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences.
Briefings Bioinform.
Rulan Wang, Chia-Ru Chung, Hsien-Da Huang, Tzong-Yi Lee
2023 J jnl
KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites.
Genom. Proteom. Bioinform.
Renfei Ma, Shangfu Li, Wenshuo Li, Lantian Yao, Hsien-Da Huang, Tzong-Yi Lee
2023 J jnl
Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis.
Briefings Bioinform.
Yigang Chen, Yang-Chi-Dung Lin, Yijun Luo, Xiao-Xuan Cai, Peng Qiu, Shi-Dong Cui, Zhe Wang, Hsi-Yuan Huang, Hsien-Da Huang
2022 J jnl
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers.
Nucleic Acids Res.
Yigang 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
2022 J jnl
On the force field optimisation of β-lactam cores using the force field Toolkit.
J. Comput. Aided Mol. Des.
Qiyang Wu, Tianyang Huang, Songyan Xia, Frank Otto, Tzong-Yi Lee, Hsien-Da Huang, Ying-Chih Chiang
2022 J jnl
dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications.
Nucleic Acids Res.
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
2022 J jnl
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions.
Nucleic Acids Res.
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, Yigang 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
2021 J jnl
MethHC 2.0: information repository of DNA methylation and gene expression in human cancer.
Nucleic Acids Res.
Hsi-Yuan Huang, Jing Li, Yun Tang, Yixian Huang, Yigang 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
2020 J jnl
Multi-omics profiling reveals microRNA-mediated insulin signaling networks.
BMC Bioinform.
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
2020 J jnl
miRTarBase 2020: updates to the experimentally validated microRNA?target interaction database.
Nucleic Acids Res.
Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li, Kai-Yao Huang, Sirjana Shrestha, Hsiao-Chin Hong, Yun Tang, Yigang 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
2019 J jnl
Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model.
Bioinform.
Chengyu Liu, Yu-Chen Liu, Hsien-Da Huang, Wei Wang
2019 J jnl
dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.
Nucleic Acids Res.
Kai-Yao Huang, Tzong-Yi Lee, Hui-Ju Kao, Chen-Tse Ma, Chao-Chun Lee, Tsai-Hsuan Lin, Wen-Chi Chang, Hsien-Da Huang
2018 J jnl
Integrated microRNA and mRNA expression profile analysis of tumor-associated macrophages after exposure to single-dose irradiation.
Comput. Biol. Chem.
Wei-Hsiang Kung, Andy Chi-Lung Lee, Chi-Dung Yang, Ching-Fang Yu, Men-Yee Chiew, Fang-Hsin Chen, Hsien-Da Huang
2018 J jnl
Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis.
BMC Genom.
Yu-Chen Liu, Hsiao-Chin Hong, Chi-Dung Yang, Wei-Hsiang Lee, Hsin-Tzu Huang, Hsien-Da Huang
2018 J jnl
The aquatic animals' transcriptome resource for comparative functional analysis.
BMC Genom.
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
2018 J jnl
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions.
Nucleic Acids Res.
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
2017 J jnl
Gene expression profiling of tumor-associated macrophages after exposure to single-dose irradiation.
Comput. Biol. Chem.
Wei-Hsiang Kung, Ching-Fang Yu, Andy Chi-Lung Lee, Chi-Dung Yang, Yu-Chen Liu, Fang-Hsin Chen, Hsien-Da Huang
2017 J jnl
Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi.
BMC Genom.
Yu-Chen Liu, Wen Liang Chen, Wei-Hsiang Kung, Hsien-Da Huang
2016 J jnl
CircNet: a database of circular RNAs derived from transcriptome sequencing data.
Nucleic Acids Res.
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
2016 J jnl
PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms.
BMC Bioinform.
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
2016 J jnl
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants.
Nucleic Acids Res.
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
2016 J jnl
Transcriptome sequencing based annotation and homologous evidence based scaffolding of
BMC Genom.
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
2016 J jnl
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.
Nucleic Acids Res.
Kai-Yao Huang, Min-Gang Su, Hui-Ju Kao, Yun-Chung Hsieh, Jhih-Hua Jhong, Kuang-Hao Cheng, Hsien-Da Huang, Tzong-Yi Lee
2016 J jnl
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database.
Nucleic Acids Res.
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
2015 J jnl
Editorial.
Comput. Biol. Chem.
Hsien-Da Huang, Yi-Ping Phoebe Chen
2015 J jnl
GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes.
Bioinform.
Yi-Hsiung Chen, Chi-Dung Yang, Ching-Ping Tseng, Hsien-Da Huang, Shinn-Ying Ho
2015 J jnl
Guest Editorial for the 13th Asia Pacific Bioinformatics Conference.
IEEE ACM Trans. Comput. Biol. Bioinform.
Hsien-Da Huang, Yi-Ping Phoebe Chen
2015 J jnl
MethHC: a database of DNA methylation and gene expression in human cancer.
Nucleic Acids Res.
Wei-Yun Huang, Sheng-Da Hsu, Hsi-Yuan Huang, Yi-Ming Sun, Chih-Hung Chou, Shun-Long Weng, Hsien-Da Huang
2014 J jnl
Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing.
J. Clin. Bioinform.
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
2014 J jnl
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.
Database J. Biol. Databases Curation
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
2014 J jnl
lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome.
Comput. Biol. Chem.
Wen-Ling Chan, Hsien-Da Huang, Jan-Gowth Chang
2014 J jnl
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions.
Nucleic Acids Res.
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
2013 J jnl
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing.
BMC Genom.
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
2013 J jnl
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs.
BMC Bioinform.
Tzu-Hao Chang, Hsi-Yuan Huang, Justin Bo-Kai Hsu, Shun-Long Weng, Jorng-Tzong Horng, Hsien-Da Huang
2013 — conf
Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing.
IWBBIO
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
2013 J jnl
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.
Tzu-Hao Chang, Li-Ching Wu, Tzong-Yi Lee, Shu-Pin Chen, Hsien-Da Huang, Jorng-Tzong Horng
2013 J jnl
dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.
Nucleic Acids Res.
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
2013 J jnl
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes.
Database J. Biol. Databases Curation
Wen-Ling Chan, Wen-Kuang Yang, Hsien-Da Huang, Jan-Gowth Chang
2012 J jnl
Identifying cancer highly-expressed membrane receptors for targeted drug delivery.
Int. J. Bioinform. Res. Appl.
Wei-Chih Huang, Feng-Mao Lin, Tzu-Hao Chang, Kuang-Wen Liao, Hsien-Da Huang
2012 J jnl
dbSNO: a database of cysteine
Bioinform.
Tzong-Yi Lee, Yi-Ju Chen, Cheng-Tsung Lu, Wei-Chieh Ching, Yu-Chuan Teng, Hsien-Da Huang, Yu-Ju Chen
2011 J jnl
Characterization and prediction of mRNA polyadenylation sites in human genes.
Medical Biol. Eng. Comput.
Tzu-Hao Chang, Li-Ching Wu, Yu-Ting Chen, Hsien-Da Huang, Baw-Jhiune Liu, Kuang-Fu Cheng, Jorng-Tzong Horng
2011 J jnl
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans.
Nucleic Acids Res.
Tzong-Yi Lee, Justin Bo-Kai Hsu, Wen-Chi Chang, Hsien-Da Huang
2011 J jnl
miRTar: an integrated system for identifying miRNA-target interactions in Human.
BMC Bioinform.
Justin Bo-Kai Hsu, Chih-Min Chiu, Sheng-Da Hsu, Wei-Yun Huang, Chia-Hung Chien, Tzong-Yi Lee, Hsien-Da Huang
2011 J jnl
miRTarBase: a database curates experimentally validated microRNA-target interactions.
Nucleic Acids Res.
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
2010 J jnl
An expert system to identify co-regulated gene groups from time-lagged gene clusters using cell cycle expression data.
Expert Syst. Appl.
Li-Ching Wu, Jhih-Long Huang, Jorng-Tzong Horng, Hsien-Da Huang
2010 J jnl
N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites.
J. Comput. Chem.
Tzong-Yi Lee, Justin Bo-Kai Hsu, Feng-Mao Lin, Wen-Chi Chang, Po-Chiang Hsu, Hsien-Da Huang
2010 J jnl
Prediction of small non-coding RNA in bacterial genomes using support vector machines.
Expert Syst. Appl.
Tzu-Hao Chang, Li-Ching Wu, Jun-Hong Lin, Hsien-Da Huang, Baw-Jhiune Liu, Kuang-Fu Cheng, Jorng-Tzong Horng
2009 C conf
A Human DNA Methylation Site Predictor Based on SVM.
BIBE
Yi-Ming Sun, Wei-Li Liao, Hsien-Da Huang, Baw-Jhiune Liu, Cheng-Wei Chang, Jorng-Tzong Horng, Li-Ching Wu
2009 J jnl
An expert system to predict protein thermostability using decision tree.
Expert Syst. Appl.
Li-Cheng Wu, Jian-Xin Lee, Hsien-Da Huang, Baw-Juine Liu, Jorng-Tzong Horng
2009 J jnl
Detecting LTR structures in human genomic sequences using profile hidden Markov models.
Expert Syst. Appl.
Li-Ching Wu, Hsien-Da Huang, Yu-Chung Chang, Ying-Chun Lee, Jorng-Tzong Horng
2009 J jnl
FMM: a web server for metabolic pathway reconstruction and comparative analysis.
Nucleic Acids Res.
Chih-Hung Chou, Wen-Chi Chang, Chih-Min Chiu, Chih-Chang Huang, Hsien-Da Huang
2009 J jnl
Incorporating structural characteristics for identification of protein methylation sites.
J. Comput. Chem.
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
2009 J jnl
Incorporating support vector machine for identifying protein tyrosine sulfation sites.
J. Comput. Chem.
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
2009 C conf
RiboSW .
BIBE
Tzu-Hao Chang, Li-Ching Wu, Chi-Ta Yeh, Cheng-Wei Chang, Baw-Jhiune Liu, Hsien-Da Huang, Jorng-Tzong Horng
2009 J jnl
miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression.
BMC Bioinform.
Wei-Chi Wang, Feng-Mao Lin, Wen-Chi Chang, Kuan-Yu Lin, Hsien-Da Huang, Na-Sheng Lin
2009 J jnl
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes.
Nucleic Acids Res.
Hsi-Yuan Huang, Heng-Yi Chang, Chih-Hung Chou, Ching-Ping Tseng, Shinn-Ying Ho, Chi-Dung Yang, Yih-Wei Ju, Hsien-Da Huang
2008 J jnl
Identifying Discriminative Amino Acids Within the Hemagglutinin of Human Influenza A H5N1 Virus Using a Decision Tree.
IEEE Trans. Inf. Technol. Biomed.
Li-Ching Wu, Jorng-Tzong Horng, Hsien-Da Huang, Wei-long Chen
2008 J jnl
RNALogo: a new approach to display structural RNA alignment.
Nucleic Acids Res.
Tzu-Hao Chang, Jorng-Tzong Horng, Hsien-Da Huang
2008 J jnl
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.
Nucleic Acids Res.
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
2007 J jnl
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.
Nucleic Acids Res.
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
2007 J jnl
Primer design for multiplex PCR using a genetic algorithm.
Soft Comput.
Li-Cheng Wu, Jorng-Tzong Horng, Hsi-Yuan Huang, Feng-Mao Lin, Hsien-Da Huang, Meng-Feng Tsai
2007 J jnl
ViTa: prediction of host microRNAs targets on viruses.
Nucleic Acids Res.
Paul Wei-Che Hsu, Li-Zen Lin, Sheng-Da Hsu, Justin Bo-Kai Hsu, Hsien-Da Huang
2006 J jnl
An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints.
J. Comput. Chem.
Tzong-Yi Lee, Jorng-Tzong Horng, Hsueh-Fen Juan, Hsien-Da Huang, Li-Cheng Wu, Meng-Feng Tsai, Hsuan-Cheng Huang
2006 J jnl
Biological Data Warehousing System for Identifying Transcriptional Regulatory Sites From Gene Expressions of Microarray Data.
IEEE Trans. Inf. Technol. Biomed.
Ann-Ping Tsou, Yi-Ming Sun, Chia-Lin Liu, Hsien-Da Huang, Jorng-Tzong Horng, Meng-Feng Tsai, Baw-Jhiune Liu
2006 J jnl
Database to Dynamically Aid Probe Design for Virus Identification.
IEEE Trans. Inf. Technol. Biomed.
Feng-Mao Lin, Hsien-Da Huang, Y.-C. Chang, Ann-Ping Tsou, P.-L. Chan, L.-C. Wu, Meng-Feng Tsai, Jorng-Tzong Horng
2006 J jnl
Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures.
J. Comput. Chem.
Li-Cheng Wu, Jorng-Tzong Horng, Shir-Ly Huang, Hsien-Da Huang, Baw-Jhiune Liu
2006 J jnl
ProKware: integrated software for presenting protein structural properties in protein tertiary structures.
Nucleic Acids Res.
Jui-Hung Hung, Hsien-Da Huang, Tzong-Yi Lee
2006 J jnl
RNAMST: efficient and flexible approach for identifying RNA structural homologs.
Nucleic Acids Res.
Tzu-Hao Chang, Hsien-Da Huang, Tzu-Neng Chuang, Dray-Ming Shien, Jorng-Tzong Horng
2006 J jnl
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements.
Nucleic Acids Res.
Hsi-Yuan Huang, Chia-Hung Chien, Kuan-Hua Jen, Hsien-Da Huang
2006 J jnl
dbPTM: an information repository of protein post-translational modification.
Nucleic Acids Res.
Tzong-Yi Lee, Hsien-Da Huang, Jui-Hung Hung, Hsi-Yuan Huang, Yuh-Shyong Yang, Tzu-Hao Wang
2006 J jnl
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.
Nucleic Acids Res.
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
2005 B conf
A database to aid probe design for virus identification.
APBC
Feng-Mao Lin, Hsien-Da Huang, Yu-Chung Chang, Pak-Leong Chan, Jorng-Tzong Horng, Ming-Tat Ko
2005 J jnl
Discovering Common Structural Motifs of Ribosomal Rna Secondary Structures in Prokaryotes.
Int. J. Artif. Intell. Tools
Hsien-Da Huang, Jorng-Tzong Horng, Li-Cheng Wu, Shu-Fen Fang
2005 J jnl
Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites.
J. Comput. Chem.
Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, Li-Cheng Wu, Jorng-Tzong Horng, Ann-Ping Tsou, Kuan-Tsae Huang
2005 J jnl
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites.
Nucleic Acids Res.
Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, Jorng-Tzong Horng
2005 A conf
Primer design for multiplex PCR using a genetic algorithm.
GECCO
Feng-Mao Lin, Hsien-Da Huang, Hsi-Yuan Huang, Jorng-Tzong Horng
2005 J jnl
SpliceInfo: an information repository for mRNA alternative splicing in human genome.
Nucleic Acids Res.
Hsien-Da Huang, Jorng-Tzong Horng, Feng-Mao Lin, Yu-Chung Chang, Chen-Chia Huang
2004 J jnl
A Computational Approach to Discover Differential Cooperation of Regulartory Sites in Functionally Related Genes in Yeast Genome.
J. Inf. Sci. Eng.
Hsien-Da Huang, Jorng-Tzong Horng, Chia-Hui Chang, Tsung-Shan Tsou, Jing-Yue Hong, Baw-Jhiune Liu
2004 — conf
Identifying Transcriptional Regulatory Sites in the Human Genome Using an Integrated Computation.
ISPAN
Hsien-Da Huang, Jorng-Tzong Horng, Yi-Ming Sun, Ann-Ping Tsou, Shir-Ly Huang
2004 C conf
Identifying the Combination of Genetic Factors that Determine Susceptibility to Cervical Cancer.
BIBE
Jorng-Tzong Horng, Kai-Chih Hu, Li-Cheng Wu, Hsien-Da Huang, Horn-Cheng Lai, Ton-Yuen Chu
2004 J jnl
Identifying the combination of genetic factors that determine susceptibility to cervical cancer.
IEEE Trans. Inf. Technol. Biomed.
Jorng-Tzong Horng, Kai-Chih Hu, Li-Cheng Wu, Hsien-Da Huang, Feng-Mao Lin, Shir-Ly Huang, Horn-Cheng Lai, Ton-Yuen Chu
2004 C conf
RgS-Miner: A Biological Data Warehousing, Analyzing and Mining System for Identifying Transcriptional Regulatory Sites in Human Genome.
DEXA
Yi-Ming Sun, Hsien-Da Huang, Jorng-Tzong Horng, Shir-Ly Huang, Ann-Ping Tsou
2003 J jnl
A Data Mining Method to Predict Transcriptional Regulatory Sites Based Based on Differentially Expressed Genes in Human Genome.
J. Inf. Sci. Eng.
Hsien-Da Huang, Huei-Lin Chang, Tsung-Shan Tsou, Baw-Jhiune Liu, Jorng-Tzong Horng
2003 C conf
A Data Mining Method to Predict Transcriptional Regulatory Sites Based on Differentially Expressed Genes in Human Genome.
BIBE
Hsien-Da Huang, Huei-Lin Chang, Tsung-Shan Tsou, Baw-Jhiune Liu, Cheng-Yan Kao, Jorng-Tzong Horng
2003 J jnl
Computing motif correlations in proteins.
J. Comput. Chem.
Jorng-Tzong Horng, Hsien-Da Huang, Shih-Hsien Wang, Ming-You Chen, Shir-Ly Huang, Jenn-Kang Hwang
2003 J jnl
Database of repetitive elements in complete genomes and data mining using transcription factor binding sites.
IEEE Trans. Inf. Technol. Biomed.
Jorng-Tzong Horng, Feng-Mao Lin, J. H. Lin, Hsien-Da Huang, Baw-Jhiune Liu
2002 B conf
Devising a cost effective baseball scheduling by evolutionary algorithms.
IEEE Congress on Evolutionary Computation
Jih Tsung Yang, Hsien-Da Huang, Jorng-Tzong Horng
2002 J jnl
Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae.
Silico Biol.
Jorng-Tzong Horng, Hsien-Da Huang, Shir-Ly Huang, Ueng-Cheng Yang, Yu-Chang Chang
2002 J jnl
The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions.
J. Comput. Biol.
Jorng-Tzong Horng, Hsien-Da Huang, Ming-Hui Jin, Li-Cheng Wu, Shir-Ly Huang
2001 C conf
Discovering Common Structural Motifs from SSU 16 S Ribosomal RNA Secondary Structures.
BIBE
Hsien-Da Huang, Shu-Fen Fang, Jorng-Tzong Horng, Cheng-Yan Kao
2001 — conf
Mining Combinations of Structural Motif from SSU 16 S Ribosomal RNA Secondary Structures.
German Conference on Bioinformatics
Hsien-Da Huang, Shu-Fen Fang, Jorng-Tzong Horng
2001 — conf
Mining Putative Regulatory Elements in Gene Promoter Regions.
German Conference on Bioinformatics
Jorng-Tzong Horng, Hsien-Da Huang, Cho-Chun Huang, Cheng-Yan Kao