PPISearch: a web server for searching homologous protein-protein interactions across multiple species. - Chun-Chen Chen; Chun-Yu Lin 003; Yu-Shu Lo; Jinn-Moon Yang (Nucleic Acids Res., 2009)

PCFamily: a web server for searching homologous protein complexes. - Yu-Shu Lo; Chun-Yu Lin 003; Jinn-Moon Yang (Nucleic Acids Res., 2010)

MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. - Chun-Yu Lin 003; Yi-Wei Lin; Shang-Wen Yu; Yu-Shu Lo; Jinn-Moon Yang (Nucleic Acids Res., 2012)

Inferring homologous protein-protein interactions through pair position specific scoring matrix. - Chun-Yu Lin 003; Yung-Chiang Chen; Yu-Shu Lo; Jinn-Moon Yang (BMC Bioinform., 2013)

Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. - Takeyuki Tamura; Tatsuya Akutsu; Chun-Yu Lin 003; Jinn-Moon Yang (BIBE, 2016)

Identification of the PCa28 Gene Signature as a Predictor in Prostate Cancer. - Jung-Yu Lee 001; Si-Yu Lin; Yi-Hsuan Chuang; Sing-Han Huang; Yu-Yao Tseng; Chun-Yu Lin 003; Hung-Jung Wang; Jinn-Moon Yang (BIBE, 2018)

Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes. - Chun-Yu Lin 003; Peiying Ruan; Ruiming Li; Jinn-Moon Yang; Simon See; Tatsuya Akutsu (BIBE, 2018)

Identification of the PCA29 gene signature as a predictor in prostate cancer. - Jung-Yu Lee 001; Si-Yu Lin; Chun-Yu Lin 003; Yi-Hsuan Chuang; Sing-Han Huang; Yu-Yao Tseng; Hung-Jung Wang; Jinn-Moon Yang (J. Bioinform. Comput. Biol., 2019)

Deep learning with evolutionary and genomic profiles for identifying cancer subtypes. - Chun-Yu Lin 003; Peiying Ruan; Ruiming Li; Jinn-Moon Yang; Simon See; Jiangning Song; Tatsuya Akutsu (J. Bioinform. Comput. Biol., 2019)

Weighted minimum feedback vertex sets and implementation in human cancer genes detection. - Ruiming Li; Chun-Yu Lin 003; Weifeng Guo; Tatsuya Akutsu (BMC Bioinform., 2021)

ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites. - Pengyu Liu 002; Jiangning Song; Chun-Yu Lin 003; Tatsuya Akutsu (BMC Bioinform., 2021)

Common Attractors in Multiple Boolean Networks. - Yu Cao; Wenya Pi; Chun-Yu Lin 003; Ulrike Münzner; Masahiro Ohtomo; Tatsuya Akutsu (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

SWEET: a single-sample network inference method for deciphering individual features in disease. - Hsin-Hua Chen; Chun-Wei Hsueh; Chia-Hwa Lee; Ting-Yi Hao; Tzu-Ying Tu; Lan-Yun Chang; Jih-Chin Lee; Chun-Yu Lin 003 (Briefings Bioinform., 2023)

cuTN-QSVM: cuTensorNet-accelerated Quantum Support Vector Machine with cuQuantum SDK. - Kuan-Cheng Chen; Tai-Yue Li; Yun-Yuan Wang; Simon See; Chun-Chieh Wang; Robert Wille; Nan-Yow Chen; An-Cheng Yang; Chun-Yu Lin 003 (CoRR, 2024)

Inference of single-cell network using mutual information for scRNA-seq data analysis. - Lan-Yun Chang; Ting-Yi Hao; Wei-Jie Wang; Chun-Yu Lin 003 (BMC Bioinform., 2024)

Validating large-scale quantum machine learning: efficient simulation of quantum support vector machines using tensor networks. - Kuan-Cheng Chen; Tai-Yue Li; Yun-Yuan Wang; Simon See; Chun-Chieh Wang; Robert Wille; Nan-Yow Chen; An-Cheng Yang; Chun-Yu Lin 003 (Mach. Learn. Sci. Technol., 2025)