A Combined Evolutionary Algorithm for Real Parameters Optimization. - Jinn-Moon Yang; Cheng-Yan Kao (International Conference on Evolutionary Computation, 1996)

Applying Family Competition to Evolution Strategies for Constrained Optimization. - Jinn-Moon Yang; Ying-Ping Chen; Jorng-Tzong Horng; Cheng-Yan Kao (Evolutionary Programming, 1997)

A Continuous Genetic Algorithm for Global Optimization. - Jinn-Moon Yang; Jorng-Tzong Horng; Cheng-Yan Kao (ICGA, 1997)

A New Evolutionary Approach to Developing Neural Autonomous Agents. - Jinn-Moon Yang; Jorng-Tzong Horng; Cheng-Yan Kao (ICRA, 1998)

An Evolutionary Algorithm for Synthesizing Optical Thin-Film Designs. - Jinn-Moon Yang; Cheng-Yan Kao (PPSN, 1998)

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 (CEC, 1999)

A robust evolutionary algorithm for optical thin-film designs. - Jinn-Moon Yang; Cheng-Yen Kao (CEC, 2000)

A Genetic Algorithm for Physical Mapping Problems. - Huai-Kuang Tsai; Cheng-Yan Kao; Jinn-Moon Yang (GECCO, 2000)

An Evolutionary Algorithms to Training Neural Networks for a Two-Spiral Problem. - Jinn-Moon Yang; Cheng-Yan Kao (GECCO, 2000)

A Genetic Algorithm with Adaptive Mutations and Family Competition for Training Neural Networks. - Jinn-Moon Yang; Jorng-Tzong Horng; Cheng-Yan Kao (Int. J. Neural Syst., 2000)

Flexible ligand docking using a robust evolutionary algorithm. - Jinn-Moon Yang; Cheng-Yan Kao (J. Comput. Chem., 2000)

Integrating adaptive mutations and family competition into genetic algorithms as function optimizer. - Jinn-Moon Yang; Cheng-Yan Kao (Soft Comput., 2000)

A family competition evolutionary algorithm for automated docking of flexible ligands to proteins. - Jinn-Moon Yang; Cheng-Yan Kao (IEEE Trans. Inf. Technol. Biomed., 2000)

Integrating adaptive mutations and family competition with differential evolution for flexible ligand docking. - Jinn-Moon Yang; Jorng-Tzong Horng; Cheng-Yan Kao (CEC, 2001)

Optical Coating Designs Using the Family Competition Evolutionary Algorithm. - Jinn-Moon Yang; Jorng-Tzong Horng; Chih-Jen Lin; Cheng-Yan Kao (Evol. Comput., 2001)

A Robust Evolutionary Algorithm for Training Neural Networks. - Jinn-Moon Yang; Cheng-Yan Kao (Neural Comput. Appl., 2001)

Solving traveling salesman problems by combining global and local search mechanisms. - Huai-Kuang Tsai; Jinn-Moon Yang; Cheng-Yan Kao (IEEE Congress on Evolutionary Computation, 2002)

Applying Genetic Algorithms To Finding The Optimal Gene Order In Displaying The Microarray Data. - Huai-Kuang Tsai; Jinn-Moon Yang; Cheng-Yan Kao (GECCO, 2002)

An Evolutionary Approach for Molecular Docking. - Jinn-Moon Yang (GECCO, 2003)

Finding Regularity in Various Types of Secondary Protein Structures. - Yen-Wei Chu; Jinn-Moon Yang (J. Inf. Sci. Eng., 2003)

A pharmacophore-based evolutionary approach for screening estrogen receptor antagonists. - Jinn-Moon Yang; Tsai-Wen Shen (IEEE Congress on Evolutionary Computation, 2004)

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 (GECCO (2), 2004)

An Evolutionary Approach with Pharmacophore-Based Scoring Functions for Virtual Database Screening. - Jinn-Moon Yang; Tsai-Wei Shen; Yen-Fu Chen; Yi-Yuan Chiu (GECCO (1), 2004)

Development and evaluation of a generic evolutionary method for protein-ligand docking. - Jinn-Moon Yang (J. Comput. Chem., 2004)

Some issues of designing genetic algorithms for traveling salesman problems. - Huai-Kuang Tsai; Jinn-Moon Yang; Yuan-Fan Tsai; Cheng-Yan Kao (Soft Comput., 2004)

An Evolutionary Approach for Gene Expression Patterns. - Huai-Kuang Tsai; Jinn-Moon Yang; Yuan-Fan Tsai; Cheng-Yan Kao (IEEE Trans. Inf. Technol. Biomed., 2004)

An evolutionary algorithm for large traveling salesman problems. - Huai-Kuang Tsai; Jinn-Moon Yang; Yuan-Fang Tsai; Cheng-Yan Kao (IEEE Trans. Syst. Man Cybern. Part B, 2004)

GEMSCORE: A New Empirical Energy Function for Protein Folding. - Yi-Yuan Chiu; Jenn-Kang Hwang; Jinn-Moon Yang (CIBCB, 2005)

GEMPLS: A New QSAR Method Combining Generic Evolutionary Method and Partial Least Squares. - Yen-Chih Chen; Jinn-Moon Yang; Chi-Hung Tsai; Cheng-Yan Kao (EvoWorkshops, 2005)

Consensus Scoring Criteria for Improving Enrichment in Virtual Screening. - Jinn-Moon Yang; Yen-Fu Chen; Tsai-Wei Shen; Bruce S. Kristal; D. Frank Hsu (J. Chem. Inf. Model., 2005)

(PS)2: protein structure prediction server. - Chih-Chieh Chen; Jenn-Kang Hwang; Jinn-Moon Yang (Nucleic Acids Res., 2006)

A Gaussian Evolutionary Method for Predicting Protein-Protein Interaction Sites. - Kang-Ping Liu; Jinn-Moon Yang (EvoBIO, 2007)

Evolutionary Conservation of DNA-Contact residues in DNA-binding Domains. - Yao-Lin Chang; Huai-Kuang Tsai; Cheng-Yan Kao; Yung-Chiang Chen; Jinn-Moon Yang (IMSCCS, 2007)

3D-partner: a web server to infer interacting partners and binding models. - Yung-Chiang Chen; Yu-Shu Lo; Wen-Chang Hsu; Jinn-Moon Yang (Nucleic Acids Res., 2007)

fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. - Chi-Hua Tung; Jinn-Moon Yang (Nucleic Acids Res., 2007)

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 (ECCB, 2008)

Evolutionary Conservation and Interacting Preference for Identifying Protein-DNA Interactions. - Yao-Lin Chang; I-Hsin Liu; Cheng-Yan Kao; Jinn-Moon Yang (IMSCCS, 2008)

Evolutionary conservation of DNA-contact residues in DNA-binding domains. - Yao-Lin Chang; Huai-Kuang Tsai; Cheng-Yan Kao; Yung-Chiang Chen; Yuh-Jyh Hu; Jinn-Moon Yang (BMC Bioinform., 2008)

Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations. - Yi-Yuan Chiu; Jenn-Kang Hwang; Jinn-Moon Yang (J. Comput. Chem., 2008)

ATRIPPI: An Atom-residue Preference Scoring Function for Protein-protein Interactions. - Kang-Ping Liu; Lu-Shian Chang; Jinn-Moon Yang (BIBE, 2009)

3D-interologs: A Protein-Protein Interacting Evolution Database across Multiple Species. - Jinn-Moon Yang; Yung-Chiang Chen; Yu-Shu Lo (IJCBS, 2009)

(PS)2-v2: template-based protein structure prediction server. - Chih-Chieh Chen; Jenn-Kang Hwang; Jinn-Moon Yang (BMC Bioinform., 2009)

Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses. - Jhang-Wei Huang; Chwan-Chuen King; Jinn-Moon Yang (BMC Bioinform., 2009)

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)

Template-based scoring functions for visualizing biological insights of H-2Kb-peptide-TCR complexes. - I-Hsin Liu; Yu-Shu Lo; Jinn-Moon Yang (BIBM, 2010)

Atrippi: an Atom-Residue Preference Scoring Function for protein-protein Interactions. - Kang-Ping Liu; Kai-Cheng Hsu; Jhang-Wei Huang; Lu-Shian Chang; Jinn-Moon Yang (Int. J. Artif. Intell. Tools, 2010)

SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties. - Yen-Fu Chen; Kai-Cheng Hsu; Shen-Rong Lin; Wen-Ching Wang; Yu-Chi Huang; Jinn-Moon Yang (Nucleic Acids Res., 2010)

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

iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis. - Kai-Cheng Hsu; Yen-Fu Chen; Shen-Rong Lin; Jinn-Moon Yang (BMC Bioinform., 2011)

Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses. - Jhang-Wei Huang; Jinn-Moon Yang (BMC Bioinform., 2011)

LigSeeSVM: Ligand-based virtual Screening using Support Vector Machines and data fusion. - Yen-Fu Chen; Kai-Cheng Hsu; Po-Tsun Lin; D. Frank Hsu; Bruce S. Kristal; Jinn-Moon Yang (Int. J. Comput. Biol. Drug Des., 2011)

PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes. - I-Hsin Liu; Yu-Shu Lo; Jinn-Moon Yang (Nucleic Acids Res., 2011)

GemAffinity: a scoring function for predicting binding affinity and Virtual Screening. - Kai-Cheng Hsu; Yen-Fu Chen; Jinn-Moon Yang (Int. J. Data Min. Bioinform., 2012)

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)

Template-based scoring functions for visualising biological insights of H-2Kb-peptide-TCR complexes. - I-Hsin Liu; Yu-Shu Lo; Jinn-Moon Yang (Int. J. Data Min. Bioinform., 2013)

Moiety-Linkage Map Reveals Selective Nonbisphosphonate Inhibitors of Human Geranylgeranyl Diphosphate Synthase. - Shih-Hsun Chen; Sheng-Wei Lin; Shen-Rong Lin; Po-Huang Liang; Jinn-Moon Yang (J. Chem. Inf. Model., 2013)

KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. - Yi-Yuan Chiu; Chih-Ta Lin; Jhang-Wei Huang; Kai-Cheng Hsu; Jen-Hu Tseng; Syuan-Ren You; Jinn-Moon Yang (Nucleic Acids Res., 2013)

Pathway-based Screening Strategy for Multitarget Inhibitors of Diverse Proteins in Metabolic Pathways. - Kai-Cheng Hsu; Wen-Chi Cheng; Yen-Fu Chen; Wen-Ching Wang; Jinn-Moon Yang (PLoS Comput. Biol., 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)

Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection. - Nikhil Pathak; Mei-Ling Lai; Wen-Yu Chen; Betty-Wu Hsieh; Guann-Yi Yu; Jinn-Moon Yang (BMC Bioinform., 2017)

An integrated approach with new strategies for QSAR models and lead optimization. - Hui-Hui Hsu; Yen-Chao Hsu; Li-Jen Chang; Jinn-Moon Yang (BMC Genom., 2017)

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)

A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. - Sing-Han Huang; Yu-Shu Lo; Yong-Chun Luo; Yu-Yao Tseng; Jinn-Moon Yang (BMC Syst. Biol., 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)

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 (BIBE, 2020)

FooDisNET: a database of food-compound-protein-disease associations. - Chu-Yun Lin; Jung-Yu Lee 001; Sing-Han Huang; Yen-Chao Hsu; Nung-Yu Hsu; Jinn-Moon Yang (BIBE, 2020)

CoMI: consensus mutual information for tissue-specific gene signatures. - Sing-Han Huang; Yu-Shu Lo; Yong-Chun Luo; Yi-Hsuan Chuang; Jung-Yu Lee 001; Jinn-Moon Yang (BMC Bioinform., 2021)

Pharmacophore anchor models of ATAT1 to discover potential inhibitors and lead optimization. - Nung-Yu Hsu; Nikhil Pathak; Yun-Ti Chen; Yen-Chao Hsu; Jinn-Moon Yang (Comput. Biol. Chem., 2021)

Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations. - You-Wei Fan; Wan-Hsin Liu; Yun-Ti Chen; Yen-Chao Hsu; Nikhil Pathak; Yu-Wei Huang; Jinn-Moon Yang (BMC Bioinform., 2022)

Discovery of moiety preference by Shapley value in protein kinase family using random forest models. - Yu-Wei Huang; Yen-Chao Hsu; Yi-Hsuan Chuang; Yun-Ti Chen; Xiang-Yu Lin; You-Wei Fan; Nikhil Pathak; Jinn-Moon Yang (BMC Bioinform., 2022)

Densest subgraph-based methods for protein-protein interaction hot spot prediction. - Ruiming Li; Jung-Yu Lee 001; Jinn-Moon Yang; Tatsuya Akutsu (BMC Bioinform., 2022)

Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties. - Xiang-Yu Lin; Yu-Wei Huang; You-Wei Fan; Yun-Ti Chen; Nikhil Pathak; Yen-Chao Hsu; Jinn-Moon Yang (BMC Bioinform., 2022)