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2020 – today
- 2022
[j45]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): 451 (2022)- [j44]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. 23-S(4): 130 (2022) - [j43]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. 23-S(4): 242 (2022) - [j42]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-S(4): 247 (2022) - 2021
- [j41]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. 22-S(10): 624 (2021) - [j40]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: 107513 (2021) - 2020
- [c31]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: 160-167 - [c30]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: 190-195
2010 – 2019
- 2019
- [j39]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): 1940005:1-1940005:15 (2019) - [j38]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): 1940006:1-1940006:12 (2019) - 2018
- [j37]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): 79-91 (2018) - [c29]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: 147-150 - [c28]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: 155-158 - 2017
- [j36]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): 39-51 (2017) - [j35]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) - 2016
- [c27]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: 57-63 - 2013
- [j34]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): S11 (2013) - [j33]I-Hsin Liu, Yu-Shu Lo, Jinn-Moon Yang:
Template-based scoring functions for visualising biological insights of H-2Kb-peptide-TCR complexes. Int. J. Data Min. Bioinform. 8(3): 326-337 (2013) - [j32]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): 2299-2311 (2013) - [j31]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): 430-440 (2013) - [j30]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) - 2012
- [j29]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): 27-41 (2012) - [j28]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): 263-270 (2012) - 2011
- [j27]Jhang-Wei Huang, Jinn-Moon Yang:
Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses. BMC Bioinform. 12(S-1): S31 (2011) - [j26]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): S33 (2011) - [j25]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): 274-289 (2011) - [j24]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): 254-260 (2011) - 2010
- [j23]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): 251-266 (2010) - [j22]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): 424-430 (2010) - [j21]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): 516-522 (2010) - [c26]I-Hsin Liu, Yu-Shu Lo, Jinn-Moon Yang:
Template-based scoring functions for visualizing biological insights of H-2Kb-peptide-TCR complexes. BIBM 2010: 127-132
2000 – 2009
- 2009
- [j20]Chih-Chieh Chen, Jenn-Kang Hwang, Jinn-Moon Yang:
(PS)2-v2: template-based protein structure prediction server. BMC Bioinform. 10: 366 (2009) - [j19]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) - [j18]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): 369-375 (2009) - [c25]Kang-Ping Liu, Lu-Shian Chang, Jinn-Moon Yang:
ATRIPPI: An Atom-residue Preference Scoring Function for Protein-protein Interactions. BIBE 2009: 392-399 - [c24]Kai-Cheng Hsu, Yen-Fu Chen, Jinn-Moon Yang:
GemAffinity: A Scoring Function for Predicting Binding Affinity and Virtual Screening. BIBM 2009: 309-314 - [c23]Jinn-Moon Yang, Yung-Chiang Chen, Yu-Shu Lo:
3D-interologs: A Protein-Protein Interacting Evolution Database across Multiple Species. IJCBS 2009: 278-285 - 2008
- [j17]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) - [j16]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): 1364-1373 (2008) - [c22]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: 14-20 - [c21]Yao-Lin Chang, I-Hsin Liu, Cheng-Yan Kao, Jinn-Moon Yang:
Evolutionary Conservation and Interacting Preference for Identifying Protein-DNA Interactions. IMSCCS 2008: 1-8 - 2007
- [j15]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): 438-443 (2007) - [j14]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): 561-567 (2007) - [c20]Kang-Ping Liu, Jinn-Moon Yang:
A Gaussian Evolutionary Method for Predicting Protein-Protein Interaction Sites. EvoBIO 2007: 143-154 - [c19]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: 9-16 - 2006
- [j13]Chih-Chieh Chen, Jenn-Kang Hwang, Jinn-Moon Yang:
(PS)2: protein structure prediction server. Nucleic Acids Res. 34(Web-Server-Issue): 152-157 (2006) - 2005
- [j12]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): 1134-1146 (2005) - [c18]Yi-Yuan Chiu, Jenn-Kang Hwang, Jinn-Moon Yang:
GEMSCORE: A New Empirical Energy Function for Protein Folding. CIBCB 2005: 303-310 - [c17]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: 125-135 - 2004
- [j11]Jinn-Moon Yang:
Development and evaluation of a generic evolutionary method for protein-ligand docking. J. Comput. Chem. 25(6): 843-857 (2004) - [j10]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): 689-697 (2004) - [j9]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): 69-78 (2004) - [j8]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): 1718-1729 (2004) - [c16]Jinn-Moon Yang, Tsai-Wen Shen:
A pharmacophore-based evolutionary approach for screening estrogen receptor antagonists. IEEE Congress on Evolutionary Computation 2004: 1028-1035 - [c15]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: 385-386 - [c14]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: 481-492 - 2003
- [j7]Yen-Wei Chu, Jinn-Moon Yang:
Finding Regularity in Various Types of Secondary Protein Structures. J. Inf. Sci. Eng. 19(6): 943-952 (2003) - [c13]Jinn-Moon Yang:
An Evolutionary Approach for Molecular Docking. GECCO 2003: 2372-2383 - 2002
- [c12]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: 1290-1295 - [c11]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: 610-617 - 2001
- [j6]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): 421-443 (2001) - [j5]Jinn-Moon Yang, Cheng-Yan Kao:
A Robust Evolutionary Algorithm for Training Neural Networks. Neural Comput. Appl. 10(3): 214-230 (2001) - [c10]Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao:
Integrating adaptive mutations and family competition with differential evolution for flexible ligand docking. CEC 2001: 473-480 - 2000
- [j4]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): 333-352 (2000) - [j3]Jinn-Moon Yang, Cheng-Yan Kao:
Flexible ligand docking using a robust evolutionary algorithm. J. Comput. Chem. 21(11): 988 (2000) - [j2]Jinn-Moon Yang, Cheng-Yan Kao:
Integrating adaptive mutations and family competition into genetic algorithms as function optimizer. Soft Comput. 4(2): 89-102 (2000) - [j1]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): 225-237 (2000) - [c9]Jinn-Moon Yang, Cheng-Yen Kao:
A robust evolutionary algorithm for optical thin-film designs. CEC 2000: 978-985 - [c8]Huai-Kuang Tsai, Cheng-Yan Kao, Jinn-Moon Yang:
A Genetic Algorithm for Physical Mapping Problems. GECCO 2000: 375 - [c7]Jinn-Moon Yang, Cheng-Yan Kao:
An Evolutionary Algorithms to Training Neural Networks for a Two-Spiral Problem. GECCO 2000: 1025-1032
1990 – 1999
- 1999
- [c6]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: 1994-2001 - 1998
- [c5]Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao:
A New Evolutionary Approach to Developing Neural Autonomous Agents. ICRA 1998: 1411-1416 - [c4]Jinn-Moon Yang, Cheng-Yan Kao:
An Evolutionary Algorithm for Synthesizing Optical Thin-Film Designs. PPSN 1998: 947-958 - 1997
- [c3]Jinn-Moon Yang, Ying-Ping Chen, Jorng-Tzong Horng, Cheng-Yan Kao:
Applying Family Competition to Evolution Strategies for Constrained Optimization. Evolutionary Programming 1997: 201-211 - [c2]Jinn-Moon Yang, Jorng-Tzong Horng, Cheng-Yan Kao:
A Continuous Genetic Algorithm for Global Optimization. ICGA 1997: 230-237 - 1996
- [c1]Jinn-Moon Yang, Cheng-Yan Kao:
A Combined Evolutionary Algorithm for Real Parameters Optimization. International Conference on Evolutionary Computation 1996: 732-737
Coauthor Index
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