Discovering Common Structural Motifs from SSU 16 S Ribosomal RNA Secondary Structures. - Hsien-Da Huang; Shu-Fen Fang; Jorng-Tzong Horng; Cheng-Yan Kao (BIBE, 2001)

Mining Putative Regulatory Elements in Gene Promoter Regions. - Jorng-Tzong Horng; Hsien-Da Huang; Cho-Chun Huang; Cheng-Yan Kao (German Conference on Bioinformatics, 2001)

Mining Combinations of Structural Motif from SSU 16 S Ribosomal RNA Secondary Structures. - Hsien-Da Huang; Shu-Fen Fang; Jorng-Tzong Horng (German Conference on Bioinformatics, 2001)

Devising a cost effective baseball scheduling by evolutionary algorithms. - Jih Tsung Yang; Hsien-Da Huang; Jorng-Tzong Horng (IEEE Congress on Evolutionary Computation, 2002)

Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae. - Jorng-Tzong Horng; Hsien-Da Huang; Shir-Ly Huang; Ueng-Cheng Yang; Yu-Chang Chang (Silico Biol., 2002)

The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions. - Jorng-Tzong Horng; Hsien-Da Huang; Ming-Hui Jin; Li-Cheng Wu; Shir-Ly Huang (J. Comput. Biol., 2002)

A Data Mining Method to Predict Transcriptional Regulatory Sites Based on Differentially Expressed Genes in Human Genome. - Hsien-Da Huang; Huei-Lin Chang; Tsung-Shan Tsou; Baw-Jhiune Liu; Cheng-Yan Kao; Jorng-Tzong Horng (BIBE, 2003)

Computing motif correlations in proteins. - Jorng-Tzong Horng; Hsien-Da Huang; Shih-Hsien Wang; Ming-You Chen; Shir-Ly Huang; Jenn-Kang Hwang (J. Comput. Chem., 2003)

A Data Mining Method to Predict Transcriptional Regulatory Sites Based Based on Differentially Expressed Genes in Human Genome. - Hsien-Da Huang; Huei-Lin Chang; Tsung-Shan Tsou; Baw-Jhiune Liu; Jorng-Tzong Horng (J. Inf. Sci. Eng., 2003)

Database of repetitive elements in complete genomes and data mining using transcription factor binding sites. - Jorng-Tzong Horng; Feng-Mao Lin; J. H. Lin; Hsien-Da Huang; Baw-Jhiune Liu (IEEE Trans. Inf. Technol. Biomed., 2003)

Identifying the Combination of Genetic Factors that Determine Susceptibility to Cervical Cancer. - Jorng-Tzong Horng; Kai-Chih Hu; Li-Cheng Wu; Hsien-Da Huang; Horn-Cheng Lai; Ton-Yuen Chu (BIBE, 2004)

RgS-Miner: A Biological Data Warehousing, Analyzing and Mining System for Identifying Transcriptional Regulatory Sites in Human Genome. - Yi-Ming Sun; Hsien-Da Huang; Jorng-Tzong Horng; Shir-Ly Huang; Ann-Ping Tsou (DEXA, 2004)

Identifying Transcriptional Regulatory Sites in the Human Genome Using an Integrated Computation. - Hsien-Da Huang; Jorng-Tzong Horng; Yi-Ming Sun; Ann-Ping Tsou; Shir-Ly Huang (ISPAN, 2004)

A Computational Approach to Discover Differential Cooperation of Regulartory Sites in Functionally Related Genes in Yeast Genome. - Hsien-Da Huang; Jorng-Tzong Horng; Chia-Hui Chang; Tsung-Shan Tsou; Jing-Yue Hong; Baw-Jhiune Liu (J. Inf. Sci. Eng., 2004)

Identifying the combination of genetic factors that determine susceptibility to cervical cancer. - Jorng-Tzong Horng; Kai-Chih Hu; Li-Cheng Wu; Hsien-Da Huang; Feng-Mao Lin; Shir-Ly Huang; Horn-Cheng Lai; Ton-Yuen Chu (IEEE Trans. Inf. Technol. Biomed., 2004)

A database to aid probe design for virus identification. - Feng-Mao Lin; Hsien-Da Huang; Yu-Chung Chang; Pak-Leong Chan; Jorng-Tzong Horng; Ming-Tat Ko (APBC, 2005)

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

Discovering Common Structural Motifs of Ribosomal Rna Secondary Structures in Prokaryotes. - Hsien-Da Huang; Jorng-Tzong Horng; Li-Cheng Wu; Shu-Fen Fang (Int. J. Artif. Intell. Tools, 2005)

Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites. - Hsien-Da Huang; Tzong-Yi Lee; Shih-Wei Tzeng; Li-Cheng Wu; Jorng-Tzong Horng; Ann-Ping Tsou; Kuan-Tsae Huang (J. Comput. Chem., 2005)

SpliceInfo: an information repository for mRNA alternative splicing in human genome. - Hsien-Da Huang; Jorng-Tzong Horng; Feng-Mao Lin; Yu-Chung Chang; Chen-Chia Huang (Nucleic Acids Res., 2005)

KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. - Hsien-Da Huang; Tzong-Yi Lee; Shih-Wei Tzeng; Jorng-Tzong Horng (Nucleic Acids Res., 2005)

An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints. - Tzong-Yi Lee; Jorng-Tzong Horng; Hsueh-Fen Juan; Hsien-Da Huang; Li-Cheng Wu; Meng-Feng Tsai; Hsuan-Cheng Huang (J. Comput. Chem., 2006)

Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures. - Li-Cheng Wu; Jorng-Tzong Horng; Shir-Ly Huang; Hsien-Da Huang; Baw-Jhiune Liu (J. Comput. Chem., 2006)

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)

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. - 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 (Nucleic Acids Res., 2006)

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)

ProKware: integrated software for presenting protein structural properties in protein tertiary structures. - Jui-Hung Hung; Hsien-Da Huang; Tzong-Yi Lee (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)

Database to Dynamically Aid Probe Design for Virus Identification. - Feng-Mao Lin; Hsien-Da Huang; Y.-C. Chang; Ann-Ping Tsou; P.-L. Chan; L.-C. Wu; Meng-Feng Tsai; Jorng-Tzong Horng (IEEE Trans. Inf. Technol. Biomed., 2006)

Biological Data Warehousing System for Identifying Transcriptional Regulatory Sites From Gene Expressions of Microarray Data. - Ann-Ping Tsou; Yi-Ming Sun; Chia-Lin Liu; Hsien-Da Huang; Jorng-Tzong Horng; Meng-Feng Tsai; Baw-Jhiune Liu (IEEE Trans. Inf. Technol. Biomed., 2006)

ViTa: prediction of host microRNAs targets on viruses. - Paul Wei-Che Hsu; Li-Zen Lin; Sheng-Da Hsu; Justin Bo-Kai Hsu; Hsien-Da Huang (Nucleic Acids Res., 2007)

KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. - 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 (Nucleic Acids Res., 2007)

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)

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

miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. - 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 (Nucleic Acids Res., 2008)

Identifying Discriminative Amino Acids Within the Hemagglutinin of Human Influenza A H5N1 Virus Using a Decision Tree. - Li-Ching Wu; Jorng-Tzong Horng; Hsien-Da Huang; Wei-Long Chen (IEEE Trans. Inf. Technol. Biomed., 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)

A Human DNA Methylation Site Predictor Based on SVM. - Yi-Ming Sun; Wei-Li Liao; Hsien-Da Huang; Baw-Jhiune Liu; Cheng-Wei Chang; Jorng-Tzong Horng; Li-Ching Wu (BIBE, 2009)

miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression. - Wei-Chi Wang; Feng-Mao Lin; Wen-Chi Chang; Kuan-Yu Lin; Hsien-Da Huang; Na-Sheng Lin (BMC Bioinform., 2009)

Detecting LTR structures in human genomic sequences using profile hidden Markov models. - Li-Ching Wu; Hsien-Da Huang; Yu-Chung Chang; Ying-Chun Lee; Jorng-Tzong Horng (Expert Syst. Appl., 2009)

An expert system to predict protein thermostability using decision tree. - Li-Cheng Wu; Jian-Xin Lee; Hsien-Da Huang; Baw-Juine Liu; Jorng-Tzong Horng (Expert Syst. Appl., 2009)

Incorporating support vector machine for identifying protein tyrosine sulfation sites. - 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 (J. Comput. Chem., 2009)

Incorporating structural characteristics for identification of protein methylation sites. - 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 (J. Comput. Chem., 2009)

FMM: a web server for metabolic pathway reconstruction and comparative analysis. - Chih-Hung Chou; Wen-Chi Chang; Chih-Min Chiu; Chih-Chang Huang; Hsien-Da Huang (Nucleic Acids Res., 2009)

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)

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)

An expert system to identify co-regulated gene groups from time-lagged gene clusters using cell cycle expression data. - Li-Ching Wu; Jhih-Long Huang; Jorng-Tzong Horng; Hsien-Da Huang (Expert Syst. Appl., 2010)

N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites. - Tzong-Yi Lee; Justin Bo-Kai Hsu; Feng-Mao Lin; Wen-Chi Chang; Po-Chiang Hsu; Hsien-Da Huang (J. Comput. Chem., 2010)

miRTar: an integrated system for identifying miRNA-target interactions in Human. - Justin Bo-Kai Hsu; Chih-Min Chiu; Sheng-Da Hsu; Wei-Yun Huang; Chia-Hung Chien; Tzong-Yi Lee; Hsien-Da Huang (BMC Bioinform., 2011)

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)

miRTarBase: a database curates experimentally validated microRNA-target interactions. - 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; et al. (Nucleic Acids Res., 2011)

RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. - Tzong-Yi Lee; Justin Bo-Kai Hsu; Wen-Chi Chang; Hsien-Da Huang (Nucleic Acids Res., 2011)

dbSNO: a database of cysteine S-nitrosylation. - Tzong-Yi Lee; Yi-Ju Chen; Cheng-Tsung Lu; Wei-Chieh Ching; Yu-Chuan Teng; Hsien-Da Huang; Yu-Ju Chen (Bioinform., 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)

pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes. - Wen-Ling Chan; Wen-Kuang Yang; Hsien-Da Huang; Jan-Gowth Chang (Database J. Biol. Databases Curation, 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)

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)

dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. - 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 (Nucleic Acids Res., 2013)

RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. - 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 (Database J. Biol. Databases Curation, 2014)

lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome. - Wen-Ling Chan; Hsien-Da Huang; Jan-Gowth 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)

GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes. - Yi-Hsiung Chen; Chi-Dung Yang; Ching-Ping Tseng; Hsien-Da Huang; Shinn-Ying Ho (Bioinform., 2015)

Editorial. - Hsien-Da Huang; Yi-Ping Phoebe Chen (Comput. Biol. Chem., 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)

Guest Editorial for the 13th Asia Pacific Bioinformatics Conference. - Hsien-Da Huang; Yi-Ping Phoebe Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms. - 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 (BMC Bioinform., 2016)

Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome. - 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 (BMC Genom., 2016)

miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. - Chih-Hung Chou; Nai-Wen Chang 001; 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; et al. (Nucleic Acids Res., 2016)

PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. - 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 (Nucleic Acids Res., 2016)

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. - Kai-Yao Huang; Min-Gang Su; Hui-Ju Kao; Yun-Chung Hsieh; Jhih-Hua Jhong; Kuang-Hao Cheng; Hsien-Da Huang; Tzong-Yi Lee (Nucleic Acids Res., 2016)

CircNet: a database of circular RNAs derived from transcriptome sequencing data. - 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 (Nucleic Acids Res., 2016)

Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi. - Yu-Chen Liu; Wen Liang Chen; Wei-Hsiang Kung; Hsien-Da Huang (BMC Genom., 2017)

Gene expression profiling of tumor-associated macrophages after exposure to single-dose irradiation. - Wei-Hsiang Kung; Ching-Fang Yu; Andy Chi-Lung Lee; Chi-Dung Yang; Yu-Chen Liu; Fang-Hsin Chen; Hsien-Da Huang (Comput. Biol. Chem., 2017)

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)

Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis. - Yu-Chen Liu; Hsiao-Chin Hong; Chi-Dung Yang; Wei-Hsiang Lee; Hsin-Tzu Huang; Hsien-Da Huang (BMC Genom., 2018)

Integrated microRNA and mRNA expression profile analysis of tumor-associated macrophages after exposure to single-dose irradiation. - Wei-Hsiang Kung; Andy Chi-Lung Lee; Chi-Dung Yang; Ching-Fang Yu; Men-Yee Chiew; Fang-Hsin Chen; Hsien-Da Huang (Comput. Biol. Chem., 2018)

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. - Chih-Hung Chou; Sirjana Shrestha; Chi-Dung Yang; Nai-Wen Chang 001; Yu-Ling Lin; Kuang-Wen Liao; Wei-Chih Huang 002; Ting-Hsuan Sun; Siang-Jyun Tu; Wei-Hsiang Lee; Men-Yee Chiew; Chun-San Tai; et al. (Nucleic Acids Res., 2018)

Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model. - Chengyu Liu; Yu-Chen Liu; Hsien-Da Huang; Wei Wang 051 (Bioinform., 2019)

dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications. - Kai-Yao Huang; Tzong-Yi Lee; Hui-Ju Kao; Chen-Tse Ma; Chao-Chun Lee; Tsai-Hsuan Lin; Wen-Chi Chang; Hsien-Da Huang (Nucleic Acids Res., 2019)

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)

On the force field optimisation of β-lactam cores using the force field Toolkit. - Qiyang Wu; Tianyang Huang; Songyan Xia; Frank Otto; Tzong-Yi Lee; Hsien-Da Huang; Ying-Chih Chiang (J. Comput. Aided Mol. Des., 2022)

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)

dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. - 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; et al. (Nucleic Acids Res., 2022)

KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites. - Renfei Ma; Shangfu Li; Wenshuo Li; Lantian Yao; Hsien-Da Huang; Tzong-Yi Lee (Genom. Proteom. Bioinform., 2023)

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)

Holistic similarity-based prediction of phosphorylation sites for understudied kinases. - Renfei Ma; Shangfu Li; Luca Parisi; Wenshuo Li; Hsien-Da Huang; Tzong-Yi Lee (Briefings Bioinform., 2023)

Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences. - Rulan Wang; Chia-Ru Chung; 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)