Jinn-Moon Yang

76 papers A* 1A 5B 5C 8Journal 45Unranked 12

Year	Rank	Type	Title / Venue / Authors
2022	J	`jnl`	Densest subgraph-based methods for protein-protein interaction hot spot prediction. BMC Bioinform. Ruiming Li, Jung-Yu Lee, Jinn-Moon Yang, Tatsuya Akutsu
2022	J	`jnl`	Discovery of moiety preference by Shapley value in protein kinase family using random forest models. BMC Bioinform. Yu-Wei Huang, Yen-Chao Hsu, Yi-Hsuan Chuang, Yun-Ti Chen, Xiang-Yu Lin, You-Wei Fan, Nikhil Pathak, Jinn-Moon Yang
2022	J	`jnl`	Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations. BMC Bioinform. You-Wei Fan, Wan-Hsin Liu, Yun-Ti Chen, Yen-Chao Hsu, Nikhil Pathak, Yu-Wei Huang, Jinn-Moon Yang
2022	J	`jnl`	Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties. BMC Bioinform. Xiang-Yu Lin, Yu-Wei Huang, You-Wei Fan, Yun-Ti Chen, Nikhil Pathak, Yen-Chao Hsu, Jinn-Moon Yang
2021	J	`jnl`	CoMI: consensus mutual information for tissue-specific gene signatures. BMC Bioinform. Sing-Han Huang, Yu-Shu Lo, Yong-Chun Luo, Yi-Hsuan Chuang, Jung-Yu Lee, Jinn-Moon Yang
2021	J	`jnl`	Pharmacophore anchor models of ATAT1 to discover potential inhibitors and lead optimization. Comput. Biol. Chem. Nung-Yu Hsu, Nikhil Pathak, Yun-Ti Chen, Yen-Chao Hsu, Jinn-Moon Yang
2020	C	`conf`	Configurational Differences and Binding Mechanisms of Interleukin-1 Receptor-Associated Kinase 1. BIBE Yun-Ti Chen, Cheng-Hsuan Wu, Yi-Cyun Chen, Yen-Chao Hsu, Yu-Wei Huang, Jinn-Moon Yang
2020	C	`conf`	FooDisNET: a database of food-compound-protein-disease associations. BIBE Chu-Yun Lin, Jung-Yu Lee, Sing-Han Huang, Yen-Chao Hsu, Nung-Yu Hsu, Jinn-Moon Yang
2019	J	`jnl`	Deep learning with evolutionary and genomic profiles for identifying cancer subtypes. J. Bioinform. Comput. Biol. Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Jiangning Song, Tatsuya Akutsu
2019	J	`jnl`	Identification of the PCA29 gene signature as a predictor in prostate cancer. J. Bioinform. Comput. Biol. Jung-Yu Lee, Si-Yu Lin, Chun-Yu Lin, Yi-Hsuan Chuang, Sing-Han Huang, Yu-Yao Tseng, Hung-Jung Wang, Jinn-Moon Yang
2018	J	`jnl`	A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. BMC Syst. Biol. Sing-Han Huang, Yu-Shu Lo, Yong-Chun Luo, Yu-Yao Tseng, Jinn-Moon Yang
2018	C	`conf`	Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes. BIBE Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Tatsuya Akutsu
2018	C	`conf`	Identification of the PCa28 Gene Signature as a Predictor in Prostate Cancer. BIBE Jung-Yu Lee, Si-Yu Lin, Yi-Hsuan Chuang, Sing-Han Huang, Yu-Yao Tseng, Chun-Yu Lin, Hung-Jung Wang, Jinn-Moon Yang
2017	J	`jnl`	An integrated approach with new strategies for QSAR models and lead optimization. BMC Genom. Hui-Hui Hsu, Yen-Chao Hsu, Li-Jen Chang, Jinn-Moon Yang
2017	J	`jnl`	Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection. BMC Bioinform. Nikhil Pathak, Mei-Ling Lai, Wen-Yu Chen, Betty-Wu Hsieh, Guann-Yi Yu, Jinn-Moon Yang
2016	C	`conf`	Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. BIBE Takeyuki Tamura, Tatsuya Akutsu, Chun-Yu Lin, Jinn-Moon Yang
2013	J	`jnl`	Inferring homologous protein-protein interactions through pair position specific scoring matrix. BMC Bioinform. Chun-Yu Lin, Yung-Chiang Chen, Yu-Shu Lo, Jinn-Moon Yang
2013	J	`jnl`	KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. Nucleic Acids Res. Yi-Yuan Chiu, Chih-Ta Lin, Jhang-Wei Huang, Kai-Cheng Hsu, Jen-Hu Tseng, Syuan-Ren You, Jinn-Moon Yang
2013	J	`jnl`	Moiety-Linkage Map Reveals Selective Nonbisphosphonate Inhibitors of Human Geranylgeranyl Diphosphate Synthase. J. Chem. Inf. Model. Shih-Hsun Chen, Sheng-Wei Lin, Shen-Rong Lin, Po-Huang Liang, Jinn-Moon Yang
2013	J	`jnl`	Pathway-based Screening Strategy for Multitarget Inhibitors of Diverse Proteins in Metabolic Pathways. PLoS Comput. Biol. Kai-Cheng Hsu, Wen-Chi Cheng, Yen-Fu Chen, Wen-Ching Wang, Jinn-Moon Yang
2013	J	`jnl`	Template-based scoring functions for visualising biological insights of H-2K Int. J. Data Min. Bioinform. I-Hsin Liu, Yu-Shu Lo, Jinn-Moon Yang
2012	J	`jnl`	GemAffinity: a scoring function for predicting binding affinity and Virtual Screening. Int. J. Data Min. Bioinform. Kai-Cheng Hsu, Yen-Fu Chen, Jinn-Moon Yang
2012	J	`jnl`	MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. Nucleic Acids Res. Chun-Yu Lin, Yi-Wei Lin, Shang-Wen Yu, Yu-Shu Lo, Jinn-Moon Yang
2011	J	`jnl`	Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses. BMC Bioinform. Jhang-Wei Huang, Jinn-Moon Yang
2011	J	`jnl`	LigSeeSVM: Ligand-based virtual Screening using Support Vector Machines and data fusion. Int. J. Comput. Biol. Drug Des. Yen-Fu Chen, Kai-Cheng Hsu, Po-Tsun Lin, D. Frank Hsu, Bruce S. Kristal, Jinn-Moon Yang
2011	J	`jnl`	PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes. Nucleic Acids Res. I-Hsin Liu, Yu-Shu Lo, Jinn-Moon Yang
2011	J	`jnl`	iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis. BMC Bioinform. Kai-Cheng Hsu, Yen-Fu Chen, Shen-Rong Lin, Jinn-Moon Yang
2010	J	`jnl`	Atrippi: an Atom-Residue Preference Scoring Function for protein-protein Interactions. Int. J. Artif. Intell. Tools Kang-Ping Liu, Kai-Cheng Hsu, Jhang-Wei Huang, Lu-Shian Chang, Jinn-Moon Yang
2010	J	`jnl`	PCFamily: a web server for searching homologous protein complexes. Nucleic Acids Res. Yu-Shu Lo, Chun-Yu Lin, Jinn-Moon Yang
2010	J	`jnl`	SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties. Nucleic Acids Res. Yen-Fu Chen, Kai-Cheng Hsu, Shen-Rong Lin, Wen-Ching Wang, Yu-Chi Huang, Jinn-Moon Yang
2010	—	`conf`	Template-based scoring functions for visualizing biological insights of H-2K BIBM I-Hsin Liu, Yu-Shu Lo, Jinn-Moon Yang
2009	J	`jnl`	(PS) BMC Bioinform. Chih-Chieh Chen, Jenn-Kang Hwang, Jinn-Moon Yang
2009	—	`conf`	3D-interologs: A Protein-Protein Interacting Evolution Database across Multiple Species. IJCBS Jinn-Moon Yang, Yung-Chiang Chen, Yu-Shu Lo
2009	C	`conf`	ATRIPPI: An Atom-residue Preference Scoring Function for Protein-protein Interactions. BIBE Kang-Ping Liu, Lu-Shian Chang, Jinn-Moon Yang
2009	J	`jnl`	Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses. BMC Bioinform. Jhang-Wei Huang, Chwan-Chuen King, Jinn-Moon Yang
2009	—	`conf`	GemAffinity: A Scoring Function for Predicting Binding Affinity and Virtual Screening. BIBM Kai-Cheng Hsu, Yen-Fu Chen, Jinn-Moon Yang
2009	J	`jnl`	PPISearch: a web server for searching homologous protein-protein interactions across multiple species. Nucleic Acids Res. Chun-Chen Chen, Chun-Yu Lin, Yu-Shu Lo, Jinn-Moon Yang
2008	—	`conf`	Evolutionary Conservation and Interacting Preference for Identifying Protein-DNA Interactions. IMSCCS Yao-Lin Chang, I-Hsin Liu, Cheng-Yan Kao, Jinn-Moon Yang
2008	J	`jnl`	Evolutionary conservation of DNA-contact residues in DNA-binding domains. BMC Bioinform. Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chiang Chen, Yuh-Jyh Hu, Jinn-Moon Yang
2008	C	`conf`	PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database. ECCB 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
2008	J	`jnl`	Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations. J. Comput. Chem. Yi-Yuan Chiu, Jenn-Kang Hwang, Jinn-Moon Yang
2007	J	`jnl`	3D-partner: a web server to infer interacting partners and binding models. Nucleic Acids Res. Yung-Chiang Chen, Yu-Shu Lo, Wen-Chang Hsu, Jinn-Moon Yang
2007	—	`conf`	A Gaussian Evolutionary Method for Predicting Protein-Protein Interaction Sites. EvoBIO Kang-Ping Liu, Jinn-Moon Yang
2007	—	`conf`	Evolutionary Conservation of DNA-Contact residues in DNA-binding Domains. IMSCCS Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chiang Chen, Jinn-Moon Yang
2007	J	`jnl`	fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. Nucleic Acids Res. Chi-Hua Tung, Jinn-Moon Yang
2006	J	`jnl`	(PS) Nucleic Acids Res. Chih-Chieh Chen, Jenn-Kang Hwang, Jinn-Moon Yang
2005	J	`jnl`	Consensus Scoring Criteria for Improving Enrichment in Virtual Screening. J. Chem. Inf. Model. Jinn-Moon Yang, Yen-Fu Chen, Tsai-Wei Shen, Bruce S. Kristal, D. Frank Hsu
2005	—	`conf`	GEMPLS: A New QSAR Method Combining Generic Evolutionary Method and Partial Least Squares. EvoWorkshops Yen-Chih Chen, Jinn-Moon Yang, Chi-Hung Tsai, Cheng-Yan Kao
2005	C	`conf`	GEMSCORE: A New Empirical Energy Function for Protein Folding. CIBCB Yi-Yuan Chiu, Jenn-Kang Hwang, Jinn-Moon Yang
2004	B	`conf`	A pharmacophore-based evolutionary approach for screening estrogen receptor antagonists. IEEE Congress on Evolutionary Computation Jinn-Moon Yang, Tsai-Wen Shen
2004	J	`jnl`	An Evolutionary Approach for Gene Expression Patterns. IEEE Trans. Inf. Technol. Biomed. Huai-Kuang Tsai, Jinn-Moon Yang, Yuan-Fan Tsai, Cheng-Yan Kao
2004	—	`conf`	An Evolutionary Approach with Pharmacophore-Based Scoring Functions for Virtual Database Screening. GECCO (1) Jinn-Moon Yang, Tsai-Wei Shen, Yen-Fu Chen, Yi-Yuan Chiu
2004	J	`jnl`	An evolutionary algorithm for large traveling salesman problems. IEEE Trans. Syst. Man Cybern. Part B Huai-Kuang Tsai, Jinn-Moon Yang, Yuan-Fang Tsai, Cheng-Yan Kao
2004	—	`conf`	Comparative Molecular Binding Energy Analysis of HIV-1 Protease Inhibitors Using Genetic Algorithm-Based Partial Least Squares Method. GECCO (2) Yen-Chih Chen, Jinn-Moon Yang, Chi-Hung Tsai, Cheng-Yan Kao
2004	J	`jnl`	Development and evaluation of a generic evolutionary method for protein-ligand docking. J. Comput. Chem. Jinn-Moon Yang
2004	J	`jnl`	Some issues of designing genetic algorithms for traveling salesman problems. Soft Comput. Huai-Kuang Tsai, Jinn-Moon Yang, Yuan-Fan Tsai, Cheng-Yan Kao
2003	A	`conf`	An Evolutionary Approach for Molecular Docking. GECCO Jinn-Moon Yang
2003	J	`jnl`	Finding Regularity in Various Types of Secondary Protein Structures. J. Inf. Sci. Eng. Yen-Wei Chu, Jinn-Moon Yang
2002	A	`conf`	Applying Genetic Algorithms To Finding The Optimal Gene Order In Displaying The Microarray Data. GECCO Huai-Kuang Tsai, Jinn-Moon Yang, Cheng-Yan Kao
2002	B	`conf`	Solving traveling salesman problems by combining global and local search mechanisms. IEEE Congress on Evolutionary Computation Huai-Kuang Tsai, Jinn-Moon Yang, Cheng-Yan Kao
2001	J	`jnl`	A Robust Evolutionary Algorithm for Training Neural Networks. Neural Comput. Appl. Jinn-Moon Yang, Cheng-Yan Kao
2001	B	`conf`	Integrating adaptive mutations and family competition with differential evolution for flexible ligand docking. CEC Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao
2001	J	`jnl`	Optical Coating Designs Using the Family Competition Evolutionary Algorithm. Evol. Comput. Jinn-Moon Yang, Jorng-Tzong Horng, Chih-Jen Lin, Cheng-Yan Kao
2000	A	`conf`	A Genetic Algorithm for Physical Mapping Problems. GECCO Huai-Kuang Tsai, Cheng-Yan Kao, Jinn-Moon Yang
2000	J	`jnl`	A Genetic Algorithm with Adaptive Mutations and Family Competition for Training Neural Networks. Int. J. Neural Syst. Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao
2000	J	`jnl`	A family competition evolutionary algorithm for automated docking of flexible ligands to proteins. IEEE Trans. Inf. Technol. Biomed. Jinn-Moon Yang, Cheng-Yan Kao
2000	B	`conf`	A robust evolutionary algorithm for optical thin-film designs. CEC Jinn-Moon Yang, Cheng-Yen Kao
2000	A	`conf`	An Evolutionary Algorithms to Training Neural Networks for a Two-Spiral Problem. GECCO Jinn-Moon Yang, Cheng-Yan Kao
2000	J	`jnl`	Flexible ligand docking using a robust evolutionary algorithm. J. Comput. Chem. Jinn-Moon Yang, Cheng-Yan Kao
2000	J	`jnl`	Integrating adaptive mutations and family competition into genetic algorithms as function optimizer. Soft Comput. Jinn-Moon Yang, Cheng-Yan Kao
1999	B	`conf`	Incorporation family competition into Gaussian and Cauchy mutations to training neural networks using an evolutionary algorithm. CEC Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yen Kao
1998	A*	`conf`	A New Evolutionary Approach to Developing Neural Autonomous Agents. ICRA Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao
1998	A	`conf`	An Evolutionary Algorithm for Synthesizing Optical Thin-Film Designs. PPSN Jinn-Moon Yang, Cheng-Yan Kao
1997	—	`conf`	A Continuous Genetic Algorithm for Global Optimization. ICGA Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao
1997	—	`conf`	Applying Family Competition to Evolution Strategies for Constrained Optimization. Evolutionary Programming Jinn-Moon Yang, Ying-Ping Chen, Jorng-Tzong Horng, Cheng-Yan Kao
1996	—	`conf`	A Combined Evolutionary Algorithm for Real Parameters Optimization. International Conference on Evolutionary Computation Jinn-Moon Yang, Cheng-Yan Kao