An Efficient Mechanism for Prediction of Protein-Ligand Interactions Based on Analysis of Protein Tertiary Substructures. - Darby Tien-Hao Chang; Chien-Yu Chen 001; Yen-Jen Oyang; Hsueh-Fen Juan; Hsuan-Cheng Huang (BIBE, 2004)

GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data. - Chia-Chin Wu; Hsuan-Cheng Huang; Hsueh-Fen Juan; Shui-Tein Chen (Bioinform., 2004)

ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures. - Darby Tien-Hao Chang; Chien-Yu Chen 001; Wen-Chin Chung; Yen-Jen Oyang; Hsueh-Fen Juan; Hsuan-Cheng Huang (Nucleic Acids Res., 2004)

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)

MeInfoText: associated gene methylation and cancer information from text mining. - Yu-Ching Fang; Hsuan-Cheng Huang; Hsueh-Fen Juan (BMC Bioinform., 2008)

Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis. - Timothy H. Wu; Ian Chang; Lichieh Julie Chu; Hsuan-Cheng Huang; Wailap V. Ng (BMC Bioinform., 2010)

Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy. - Chen-Ching Lin; Jen-Tsung Hsiang; Chia-Yi Wu; Yen-Jen Oyang; Hsueh-Fen Juan; Hsuan-Cheng Huang (BMC Syst. Biol., 2010)

Prediction of Essential Genes by Mining Gene Ontology Semantics. - Yu-Cheng Liu; Po-I Chiu; Hsuan-Cheng Huang; Vincent S. Tseng (ISBRA, 2011)

Coregulation of transcription factors and microRNAs in human transcriptional regulatory network. - Cho-Yi Chen; Shui-Tein Chen; Chiou-Shann Fuh; Hsueh-Fen Juan; Hsuan-Cheng Huang (BMC Bioinform., 2011)

Integrative network analysis reveals active microRNAs and their functions in gastric cancer. - Chien-Wei Tseng; Chen-Ching Lin; Chiung-Nien Chen; Hsuan-Cheng Huang; Hsueh-Fen Juan (BMC Syst. Biol., 2011)

Lengthening of 3′UTR increases with morphological complexity in animal evolution. - Cho-Yi Chen; Shui-Tein Chen; Hsueh-Fen Juan; Hsuan-Cheng Huang (Bioinform., 2012)

Crosstalk between transcription factors and microRNAs in human protein interaction network. - Chen-Ching Lin; Ya-Jen Chen; Cho-Yi Chen; Yen-Jen Oyang; Hsueh-Fen Juan; Hsuan-Cheng Huang (BMC Syst. Biol., 2012)

ValidNESs: a database of validated leucine-rich nuclear export signals. - Szu-Chin Fu; Hsuan-Cheng Huang; Paul Horton; Hsueh-Fen Juan (Nucleic Acids Res., 2013)

Mirin: identifying microRNA regulatory modules in protein-protein interaction networks. - Ken-Chi Yang; Chia-Lang Hsu; Chen-Ching Lin; Hsueh-Fen Juan; Hsuan-Cheng Huang (Bioinform., 2014)

Circadian systems biology in Metazoa. - Li-Ling Lin; Hsuan-Cheng Huang; Hsueh-Fen Juan (Briefings Bioinform., 2015)

DynaPho: a web platform for inferring the dynamics of time-series phosphoproteomics. - Chia-Lang Hsu; Jiankai Wang; Pei-Chun Lu; Hsuan-Cheng Huang; Hsueh-Fen Juan (Bioinform., 2017)

Regulatory feedback loops bridge the human gene regulatory network and regulate carcinogenesis. - Yun-Ru Chen; Hsuan-Cheng Huang; Chen-Ching Lin (Briefings Bioinform., 2019)

Refined Prediction of Mouse and Human Actions Based on A Data-Selective Multiple-Stage Approach of 3D Convolutional Neural Networks. - Chia-Ying Wu; Arthur Chun-Chieh Shih; Hsuan-Cheng Huang; Chun-Ping Yu; Chien-Chang Chen (TAAI, 2020)

DockCoV2: a drug database against SARS-CoV-2. - Ting-Fu Chen; Yu-Chuan Chang; Yi Hsiao; Ko-Han Lee; Yu-Chun Hsiao; Yu-Hsiang Lin; Yi-Chin Ethan Tu; Hsuan-Cheng Huang; Chien-Yu Chen 001; Hsueh-Fen Juan (Nucleic Acids Res., 2021)

Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis. - Kuei-Yueh Ko; Cho-Yi Chen; Hsueh-Fen Juan; Hsuan-Cheng Huang (Bioinform., 2022)

BIC: a database for the transcriptional landscape of bacteria in cancer. - Kai-Pu Chen; Chia-Lang Hsu; Yen-Jen Oyang; Hsuan-Cheng Huang; Hsueh-Fen Juan (Nucleic Acids Res., 2023)

Context-dependent gene regulatory network reveals regulation dynamics and cell trajectories using unspliced transcripts. - Yueh-Hua Tu; Hsueh-Fen Juan; Hsuan-Cheng Huang (Briefings Bioinform., 2023)