| 2020 | BIBE | Configurational Differences and Binding Mechanisms of Interleukin-1 Receptor-Associated Kinase 1. | Yun-Ti Chen, Cheng-Hsuan Wu, Yi-Cyun Chen, Yen-Chao Hsu, Yu-Wei Huang, Jinn-Moon Yang |
| 2020 | BIBE | FooDisNET: a database of food-compound-protein-disease associations. | Chu-Yun Lin, Jung-Yu Lee, Sing-Han Huang, Yen-Chao Hsu, Nung-Yu Hsu, Jinn-Moon Yang |
| 2018 | BIBE | Identification of the PCa28 Gene Signature as a Predictor in Prostate Cancer. | Jung-Yu Lee, Si-Yu Lin, Yi-Hsuan Chuang, Sing-Han Huang, Yu-Yao Tseng, Chun-Yu Lin, Hung-Jung Wang, Jinn-Moon Yang |
| 2018 | BIBE | Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes. | Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Tatsuya Akutsu |
| 2016 | BIBE | Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. | Takeyuki Tamura, Tatsuya Akutsu, Chun-Yu Lin, Jinn-Moon Yang |
| 2009 | BIBE | ATRIPPI: An Atom-residue Preference Scoring Function for Protein-protein Interactions. | Kang-Ping Liu, Lu-Shian Chang, Jinn-Moon Yang |
| 2008 | ECCB | PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database. | Chia-Ying Yang, Chao-Hui Chang, Ya-Ling Yu, Tsu-Chun Emma Lin, Sheng-An Lee, Chueh-Chuan Yen, Jinn-Moon Yang, Jin-Mei Lai, Yi-Ren Hong, Tzu-Ling Tseng, Kun-Mao Chao, Chi-Ying F. Huang |
| 2005 | CIBCB | GEMSCORE: A New Empirical Energy Function for Protein Folding. | Yi-Yuan Chiu, Jenn-Kang Hwang, Jinn-Moon Yang |
| 2004 | CEC | A pharmacophore-based evolutionary approach for screening estrogen receptor antagonists. | Jinn-Moon Yang, Tsai-Wen Shen |
| 2004 | GECCO | Comparative Molecular Binding Energy Analysis of HIV-1 Protease Inhibitors Using Genetic Algorithm-Based Partial Least Squares Method. | Yen-Chih Chen, Jinn-Moon Yang, Chi-Hung Tsai, Cheng-Yan Kao |
| 2004 | GECCO | An Evolutionary Approach with Pharmacophore-Based Scoring Functions for Virtual Database Screening. | Jinn-Moon Yang, Tsai-Wei Shen, Yen-Fu Chen, Yi-Yuan Chiu |
| 2003 | GECCO | An Evolutionary Approach for Molecular Docking. | Jinn-Moon Yang |
| 2002 | CEC | Solving traveling salesman problems by combining global and local search mechanisms. | Huai-Kuang Tsai, Jinn-Moon Yang, Cheng-Yan Kao |
| 2002 | GECCO | Applying Genetic Algorithms To Finding The Optimal Gene Order In Displaying The Microarray Data. | Huai-Kuang Tsai, Jinn-Moon Yang, Cheng-Yan Kao |
| 2001 | CEC | Integrating adaptive mutations and family competition with differential evolution for flexible ligand docking. | Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao |
| 2000 | CEC | A robust evolutionary algorithm for optical thin-film designs. | Jinn-Moon Yang, Cheng-Yen Kao |
| 2000 | GECCO | A Genetic Algorithm for Physical Mapping Problems. | Huai-Kuang Tsai, Cheng-Yan Kao, Jinn-Moon Yang |
| 2000 | GECCO | An Evolutionary Algorithms to Training Neural Networks for a Two-Spiral Problem. | Jinn-Moon Yang, Cheng-Yan Kao |
| 1999 | CEC | Incorporation family competition into Gaussian and Cauchy mutations to training neural networks using an evolutionary algorithm. | Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yen Kao |
| 1998 | ICRA | A New Evolutionary Approach to Developing Neural Autonomous Agents. | Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao |
| 1998 | PPSN | An Evolutionary Algorithm for Synthesizing Optical Thin-Film Designs. | Jinn-Moon Yang, Cheng-Yan Kao |
| 1996 | ICEC | A Combined Evolutionary Algorithm for Real Parameters Optimization. | Jinn-Moon Yang, Cheng-Yan Kao |