Jinn-Moon Yang

Publication Activity (10 Years)

Years Active: 1996-2022
Publications (10 Years): 17

Top Topics

Protein Interaction

Gene Expression Data

Top Venues

J. Bioinform. Comput. Biol.

J. Chem. Inf. Model.

Publications

Ruiming Li, Jung-Yu Lee, Jinn-Moon Yang, Tatsuya Akutsu
Densest subgraph-based methods for protein-protein interaction hot spot prediction. BMC Bioinform. 23 (1) (2022)
Xiang-Yu Lin, Yu-Wei Huang, You-Wei Fan, Yun-Ti Chen, Nikhil Pathak, Yen-Chao Hsu, Jinn-Moon Yang
Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties. BMC Bioinform. 23 (1) (2022)
Xiang-Yu Lin, Yu-Wei Huang, You-Wei Fan, Yun-Ti Chen, Nikhil Pathak, Yen-Chao Hsu, Jinn-Moon Yang
Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties. BMC Bioinform. (4) (2022)
You-Wei Fan, Wan-Hsin Liu, Yun-Ti Chen, Yen-Chao Hsu, Nikhil Pathak, Yu-Wei Huang, Jinn-Moon Yang
Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations. BMC Bioinform. (4) (2022)
Yu-Wei Huang, Yen-Chao Hsu, Yi-Hsuan Chuang, Yun-Ti Chen, Xiang-Yu Lin, You-Wei Fan, Nikhil Pathak, Jinn-Moon Yang
Discovery of moiety preference by Shapley value in protein kinase family using random forest models. BMC Bioinform. (4) (2022)
Nung-Yu Hsu, Nikhil Pathak, Yun-Ti Chen, Yen-Chao Hsu, Jinn-Moon Yang
Pharmacophore anchor models of ATAT1 to discover potential inhibitors and lead optimization. Comput. Biol. Chem. 93 (2021)
Sing-Han Huang, Yu-Shu Lo, Yong-Chun Luo, Yi-Hsuan Chuang, Jung-Yu Lee, Jinn-Moon Yang
CoMI: consensus mutual information for tissue-specific gene signatures. BMC Bioinform. (10) (2021)
Yun-Ti Chen, Cheng-Hsuan Wu, Yi-Cyun Chen, Yen-Chao Hsu, Yu-Wei Huang, Jinn-Moon Yang
Configurational Differences and Binding Mechanisms of Interleukin-1 Receptor-Associated Kinase 1. BIBE (2020)
Chu-Yun Lin, Jung-Yu Lee, Sing-Han Huang, Yen-Chao Hsu, Nung-Yu Hsu, Jinn-Moon Yang
FooDisNET: a database of food-compound-protein-disease associations. BIBE (2020)
Jung-Yu Lee, Si-Yu Lin, Chun-Yu Lin, Yi-Hsuan Chuang, Sing-Han Huang, Yu-Yao Tseng, Hung-Jung Wang, Jinn-Moon Yang
Identification of the PCA29 gene signature as a predictor in prostate cancer. J. Bioinform. Comput. Biol. 17 (3) (2019)
Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Jiangning Song, Tatsuya Akutsu
Deep learning with evolutionary and genomic profiles for identifying cancer subtypes. J. Bioinform. Comput. Biol. 17 (3) (2019)
Jung-Yu Lee, Si-Yu Lin, Yi-Hsuan Chuang, Sing-Han Huang, Yu-Yao Tseng, Chun-Yu Lin, Hung-Jung Wang, Jinn-Moon Yang
Identification of the PCa28 Gene Signature as a Predictor in Prostate Cancer. BIBE (2018)
Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Tatsuya Akutsu
Deep Learning with Evolutionary and Genomic Profiles for Identifying Cancer Subtypes. BIBE (2018)
Sing-Han Huang, Yu-Shu Lo, Yong-Chun Luo, Yu-Yao Tseng, Jinn-Moon Yang
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. BMC Syst. Biol. 12 (S-2) (2018)
Hui-Hui Hsu, Yen-Chao Hsu, Li-Jen Chang, Jinn-Moon Yang
An integrated approach with new strategies for QSAR models and lead optimization. BMC Genom. 18 (S2) (2017)
Nikhil Pathak, Mei-Ling Lai, Wen-Yu Chen, Betty-Wu Hsieh, Guann-Yi Yu, Jinn-Moon Yang
Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection. BMC Bioinform. 18 (16) (2017)
Takeyuki Tamura, Tatsuya Akutsu, Chun-Yu Lin, Jinn-Moon Yang
Finding Influential Genes Using Gene Expression Data and Boolean Models of Metabolic Networks. BIBE (2016)
Kai-Cheng Hsu, Wen-Chi Cheng, Yen-Fu Chen, Wen-Ching Wang, Jinn-Moon Yang
Pathway-based Screening Strategy for Multitarget Inhibitors of Diverse Proteins in Metabolic Pathways. PLoS Comput. Biol. 9 (7) (2013)
Yi-Yuan Chiu, Chih-Ta Lin, Jhang-Wei Huang, Kai-Cheng Hsu, Jen-Hu Tseng, Syuan-Ren You, Jinn-Moon Yang
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. Nucleic Acids Res. 41 (Database-Issue) (2013)
Chun-Yu Lin, Yung-Chiang Chen, Yu-Shu Lo, Jinn-Moon Yang
Inferring homologous protein-protein interactions through pair position specific scoring matrix. BMC Bioinform. 14 (S-2) (2013)
Shih-Hsun Chen, Sheng-Wei Lin, Shen-Rong Lin, Po-Huang Liang, Jinn-Moon Yang
Moiety-Linkage Map Reveals Selective Nonbisphosphonate Inhibitors of Human Geranylgeranyl Diphosphate Synthase. J. Chem. Inf. Model. 53 (9) (2013)
I-Hsin Liu, Yu-Shu Lo, Jinn-Moon Yang
-peptide-TCR complexes. Int. J. Data Min. Bioinform. 8 (3) (2013)
Chun-Yu Lin, Yi-Wei Lin, Shang-Wen Yu, Yu-Shu Lo, Jinn-Moon Yang
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Kai-Cheng Hsu, Yen-Fu Chen, Jinn-Moon Yang
GemAffinity: a scoring function for predicting binding affinity and Virtual Screening. Int. J. Data Min. Bioinform. 6 (1) (2012)
Kai-Cheng Hsu, Yen-Fu Chen, Shen-Rong Lin, Jinn-Moon Yang
iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis. BMC Bioinform. 12 (S-1) (2011)
Jhang-Wei Huang, Jinn-Moon Yang
Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses. BMC Bioinform. 12 (S-1) (2011)
I-Hsin Liu, Yu-Shu Lo, Jinn-Moon Yang
PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Yen-Fu Chen, Kai-Cheng Hsu, Po-Tsun Lin, D. Frank Hsu, Bruce S. Kristal, Jinn-Moon Yang
LigSeeSVM: Ligand-based virtual Screening using Support Vector Machines and data fusion. Int. J. Comput. Biol. Drug Des. 4 (3) (2011)
Kang-Ping Liu, Kai-Cheng Hsu, Jhang-Wei Huang, Lu-Shian Chang, Jinn-Moon Yang
Atrippi: an Atom-Residue Preference Scoring Function for protein-protein Interactions. Int. J. Artif. Intell. Tools 19 (3) (2010)
Yen-Fu Chen, Kai-Cheng Hsu, Shen-Rong Lin, Wen-Ching Wang, Yu-Chi Huang, Jinn-Moon Yang
SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
I-Hsin Liu, Yu-Shu Lo, Jinn-Moon Yang
-peptide-TCR complexes. BIBM (2010)
Yu-Shu Lo, Chun-Yu Lin, Jinn-Moon Yang
PCFamily: a web server for searching homologous protein complexes. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Kai-Cheng Hsu, Yen-Fu Chen, Jinn-Moon Yang
GemAffinity: A Scoring Function for Predicting Binding Affinity and Virtual Screening. BIBM (2009)
Chih-Chieh Chen, Jenn-Kang Hwang, Jinn-Moon Yang
-v2: template-based protein structure prediction server. BMC Bioinform. 10 (2009)
Kang-Ping Liu, Lu-Shian Chang, Jinn-Moon Yang
ATRIPPI: An Atom-residue Preference Scoring Function for Protein-protein Interactions. BIBE (2009)
Chun-Chen Chen, Chun-Yu Lin, Yu-Shu Lo, Jinn-Moon Yang
PPISearch: a web server for searching homologous protein-protein interactions across multiple species. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Jinn-Moon Yang, Yung-Chiang Chen, Yu-Shu Lo
3D-interologs: A Protein-Protein Interacting Evolution Database across Multiple Species. IJCBS (2009)
Jhang-Wei Huang, Chwan-Chuen King, Jinn-Moon Yang
Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses. BMC Bioinform. 10 (S-1) (2009)
Yao-Lin Chang, I-Hsin Liu, Cheng-Yan Kao, Jinn-Moon Yang
Evolutionary Conservation and Interacting Preference for Identifying Protein-DNA Interactions. IMSCCS (2008)
Yi-Yuan Chiu, Jenn-Kang Hwang, Jinn-Moon Yang
Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations. J. Comput. Chem. 29 (9) (2008)
Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chiang Chen, Yuh-Jyh Hu, Jinn-Moon Yang
Evolutionary conservation of DNA-contact residues in DNA-binding domains. BMC Bioinform. 9 (S-6) (2008)
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
PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database. ECCB (2008)
Chi-Hua Tung, Jinn-Moon Yang
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Yung-Chiang Chen, Yu-Shu Lo, Wen-Chang Hsu, Jinn-Moon Yang
3D-partner: a web server to infer interacting partners and binding models. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chiang Chen, Jinn-Moon Yang
Evolutionary Conservation of DNA-Contact residues in DNA-binding Domains. IMSCCS (2007)
Kang-Ping Liu, Jinn-Moon Yang
A Gaussian Evolutionary Method for Predicting Protein-Protein Interaction Sites. EvoBIO (2007)
Chih-Chieh Chen, Jenn-Kang Hwang, Jinn-Moon Yang
: protein structure prediction server. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Yi-Yuan Chiu, Jenn-Kang Hwang, Jinn-Moon Yang
GEMSCORE: A New Empirical Energy Function for Protein Folding. CIBCB (2005)
Jinn-Moon Yang, Yen-Fu Chen, Tsai-Wei Shen, Bruce S. Kristal, D. Frank Hsu
Consensus Scoring Criteria for Improving Enrichment in Virtual Screening. J. Chem. Inf. Model. 45 (4) (2005)
Yen-Chih Chen, Jinn-Moon Yang, Chi-Hung Tsai, Cheng-Yan Kao
GEMPLS: A New QSAR Method Combining Generic Evolutionary Method and Partial Least Squares. EvoWorkshops (2005)
Jinn-Moon Yang, Tsai-Wei Shen, Yen-Fu Chen, Yi-Yuan Chiu
An Evolutionary Approach with Pharmacophore-Based Scoring Functions for Virtual Database Screening. GECCO (1) (2004)
Jinn-Moon Yang, Tsai-Wen Shen
A pharmacophore-based evolutionary approach for screening estrogen receptor antagonists. IEEE Congress on Evolutionary Computation (2004)
Huai-Kuang Tsai, Jinn-Moon Yang, Yuan-Fan Tsai, Cheng-Yan Kao
An Evolutionary Approach for Gene Expression Patterns. IEEE Trans. Inf. Technol. Biomed. 8 (2) (2004)
Jinn-Moon Yang
Development and evaluation of a generic evolutionary method for protein-ligand docking. J. Comput. Chem. 25 (6) (2004)
Huai-Kuang Tsai, Jinn-Moon Yang, Yuan-Fan Tsai, Cheng-Yan Kao
Some issues of designing genetic algorithms for traveling salesman problems. Soft Comput. 8 (10) (2004)
Huai-Kuang Tsai, Jinn-Moon Yang, Yuan-Fang Tsai, Cheng-Yan Kao
An evolutionary algorithm for large traveling salesman problems. IEEE Trans. Syst. Man Cybern. Part B 34 (4) (2004)
Yen-Chih Chen, Jinn-Moon Yang, Chi-Hung Tsai, Cheng-Yan Kao
Comparative Molecular Binding Energy Analysis of HIV-1 Protease Inhibitors Using Genetic Algorithm-Based Partial Least Squares Method. GECCO (2) (2004)
Yen-Wei Chu, Jinn-Moon Yang
Finding Regularity in Various Types of Secondary Protein Structures. J. Inf. Sci. Eng. 19 (6) (2003)
Jinn-Moon Yang
An Evolutionary Approach for Molecular Docking. GECCO (2003)
Huai-Kuang Tsai, Jinn-Moon Yang, Cheng-Yan Kao
Solving traveling salesman problems by combining global and local search mechanisms. IEEE Congress on Evolutionary Computation (2002)
Huai-Kuang Tsai, Jinn-Moon Yang, Cheng-Yan Kao
Applying Genetic Algorithms To Finding The Optimal Gene Order In Displaying The Microarray Data. GECCO (2002)
Jinn-Moon Yang, Cheng-Yan Kao
A Robust Evolutionary Algorithm for Training Neural Networks. Neural Comput. Appl. 10 (3) (2001)
Jinn-Moon Yang, Jorng-Tzong Horng, Chih-Jen Lin, Cheng-Yan Kao
Optical Coating Designs Using the Family Competition Evolutionary Algorithm. Evol. Comput. 9 (4) (2001)
Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao
Integrating adaptive mutations and family competition with differential evolution for flexible ligand docking. CEC (2001)
Jinn-Moon Yang, Cheng-Yan Kao
An Evolutionary Algorithms to Training Neural Networks for a Two-Spiral Problem. GECCO (2000)
Jinn-Moon Yang, Cheng-Yan Kao
Integrating adaptive mutations and family competition into genetic algorithms as function optimizer. Soft Comput. 4 (2) (2000)
Jinn-Moon Yang, Cheng-Yen Kao
A robust evolutionary algorithm for optical thin-film designs. CEC (2000)
Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao
A Genetic Algorithm with Adaptive Mutations and Family Competition for Training Neural Networks. Int. J. Neural Syst. 10 (5) (2000)
Huai-Kuang Tsai, Cheng-Yan Kao, Jinn-Moon Yang
A Genetic Algorithm for Physical Mapping Problems. GECCO (2000)
Jinn-Moon Yang, Cheng-Yan Kao
A family competition evolutionary algorithm for automated docking of flexible ligands to proteins. IEEE Trans. Inf. Technol. Biomed. 4 (3) (2000)
Jinn-Moon Yang, Cheng-Yan Kao
Flexible ligand docking using a robust evolutionary algorithm. J. Comput. Chem. 21 (11) (2000)
Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yen Kao
Incorporation family competition into Gaussian and Cauchy mutations to training neural networks using an evolutionary algorithm. CEC (1999)
Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao
A New Evolutionary Approach to Developing Neural Autonomous Agents. ICRA (1998)
Jinn-Moon Yang, Cheng-Yan Kao
An Evolutionary Algorithm for Synthesizing Optical Thin-Film Designs. PPSN (1998)
Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao
A Continuous Genetic Algorithm for Global Optimization. ICGA (1997)
Jinn-Moon Yang, Ying-Ping Chen, Jorng-Tzong Horng, Cheng-Yan Kao
Applying Family Competition to Evolution Strategies for Constrained Optimization. Evolutionary Programming (1997)
Jinn-Moon Yang, Cheng-Yan Kao
A Combined Evolutionary Algorithm for Real Parameters Optimization. International Conference on Evolutionary Computation (1996)