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Name: Yang, Jinn-Moon (Professor & Director) Institute/ Department : National Chiao Tung University/ Institute of Bioinformatics In the last five years (from 2003~2008), we published 22 SCI papers, 1 non-SCI paper (PLoS ONE), and 9 conference papers. Among these 22 SCI papers, the impact factor of five papers, which I am the corresponding author, exceeds 6.0 (Figure 1A) according to the Journal Citation Reports editor 2007. On average, we publish ~4 SCI papers each year and the impact factor of each paper is 3.59. The sum of impact factors is increasing from 2005 (6.34), 2006 (13.93), 2007 (20.52) to 2008/9 (18.84). The total number of citations is 192 since 2003 and the average number of citations is 6.2 for each paper (Figure 1B). My h-index is 9 since 2000.
Figure 1. (A) The relationship between the number of papers and the impact factor and (B) the relationship between the number of citations and the publication year.
Journal Papers (* corresponding author) 1. J.-W. Huang, C.-C. King, J.-M. Yang*, "Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses," BMC Bioinformatics, in press. (IF: 3.493) 2. M.-C. Yang, H.-H. Guan, J.-M. Yang, C.-N. Ko, M.-Y. Liu, Y.-H. Lin, C.-J. Chen, and Simon JT Mao*, "Rational Design for crystallization of b-Lactoglobulin and vitamin D3 complex: reveal of a secondary binding site," Crystal Growth & Design, vol. 8, pp. 4268-4276, 2008. (IF: 4.046, one of cover stories) 3. H.-C. Hung, C.-P. Tseng, J.-M. Yang, Y.-W Ju, S.-N. Tseng, Y.-F. Chen, Y.-S. Chao, H.-P. Hsieh, S.-R. Shih, John T.-A. Hsu, "Aurintricarboxylic acid inhibits influenza virus neuraminidase," Antiviral Research, in press. (IF: 3.358) 4. Y.-Y. Chiu, J.-K. Hwang, J.-M. Yang*, "Soft energy function and generic evolutionary method for discriminating native from non-native protein conformations," Journal of Computational Chemistry, vol. 29, pp. 1364-1373, 2008 (IF: 4.297) 5. Y.-L. Chang, H.-K. Tsai, C.-Y. Kao, Y.-C. Chen, Y.-J. Hu, and J.-M. Yang*, "Evolutionary conservation of DNA-contact residues in DNA-binding domains," BMC Bioinformatics, vol. 9 (S6), pp. S3.1~S3.9, 2008 (IF: 3.493). 6. C.-Y. Yang, C.-H. Chang, T.-C. Lin, Y.-L. Yu, S.-A. Lee, C.-C. Yen, J.-M. Yang, J.-M. Lai, Y.-R. Hong, T.-L. Tseng, K.-M. Chao, and C.-Y. Huang*, "PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database," Bioinformatics, vol. 24, pp. i14-i20, 2008. (IF: 5.039) 7. M.-C. Yang, H.-H. Guan, M.-Y. Liu, Y.-H. Lin, J.-M. Yang, W.-L. Chen, C.-J. Chen, and Simon J. T. Mao*, "Crystal structure of a secondary vitamin D3 binding site of milk ß-lactoglobulin," Proteins: Structure, Function, and Bioinformatics, vol. 71, pp. 1197-1210, 2008. (IF: 3.354) 8. Y.Y. Yao, K.L. Shrestha, Y.J. Wu, H.J. Tasi, C.C. Chen, J.-M. Yang, A. Ando, C.Y. Cheng, Y.K. Li*, "Structural simulation and protein engineering to convert an endo-chitosanase to an exo-chitosanase," Protein Engineering, Design & Selection, vol. 21, pp. 561-566, 2008. (IF: 2.662) 9. C.-H. Tung, J.-W. Huang and J.-M. Yang*, "Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for fast protein structure database search," Genome Biology, vol. 8, pp. R31.1~R31.16, 2007. (IF: 6.589; Times Cited: 2) (95-2113-M-009-007- and 95-2627-B-009-001-) 10. Y.-C. Chen, Y.-S. Lo, W.-C. Hsu, and J.-M. Yang*, "3D-partner: a web server to infer interacting partners and binding models, " Nucleic Acids Research, pp. W561-W567, 2007. (IF: 6.954; Times Cited: 3) (95-2113-M-009-007- and 95-2627-B-009-001-) 11. C.-H. Tung and J.-M. Yang*, "fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies," Nucleic Acids Research, pp. W438-W443, 2007. (IF: 6.954; Times Cited: 3) (95-2113-M-009-007- and 95-2627-B-009-001-) 12. J.-M. Yang, Y.-F. Chen, Y.-Y. Tu, K.-R. Yen, and Y.-L. Yang*, “Combinatorial computation approaches identifying tetracycline derivates as flaviviruses inhibitors,” PLoS ONE, pp. e428.1- e428.12, 2007. (95-2113-M-009-007-) 13. K.-P. Liu and J.-M Yang*, "A Gaussian evolutionary method for predicting protein-protein interaction sites," Lecture Notes in Computer Science, vol. 4447, pp. 143-153, 2007. (96-2627-B-009-001-) 14. J.-M. Yang* and C.-H. Tung, "Protein structure database search and evolutionary classification," Nucleic Acids Research, vol. 34, pp. 3646-3659, 2006. (IF: 6.954; Times Cited: 10) (94-2113-M-009-014- and 94-2627-B-009-006) 15. C.-C. Chen, J.-K. Hwang and J.-M. Yang*, "(PS)2: Protein structure prediction server," Nucleic Acids Research, pp. W152–W157, 2006. (IF: 6.965; Times Cited: 3) (94-2113-M-009-014- and 94-2627-B-009-006) 16. J.-M. Yang* and T.-W. Shen, "A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators," Proteins: Structure, Function, and Bioinformatics, vol. 59, pp. 205-220, 2005. (IF: 3.354; Times Cited: 19) (94-2113-M-009-014-) 17. J.-M. Yang* Y.-F. Chen, T.-W. Shen, B. S. Kristal, and D. F. Hsu, "Consensus Scoring Criteria for Improving Enrichment in Virtual Screening," Journal of Chemical Information and Modeling, vol. 45, pp. 1134-1146, 2005. (IF: 2.986; Times Cited: 34) (94-2113-M-009-014-) 18. Y.-C. Chen, J.-M Yang, C.-H. Tsai, C.-Y. Kao, "GEMPLS: A new QSAR method combining generic evolutionary method and partial least squares", Lecture Notes in Computer Science, vol. 3449, pp. 125-135, 2005. 19. J.-M. Yang* and C.-C. Chen, "GEMDOCK: A generic evolutionary method for molecular docking," Proteins: Structure, Function, and Bioinformatics, vol. 55, pp. 288-304, 2004. (IF: 3.354; Times Cited: 37 ) 20. J.-M. Yang* "Development and evaluation of a generic evolutionary method for protein-ligand docking," Journal of Computational Chemistry, vol. 25, pp. 843-857, 2004. (IF: 4.297; Times Cited: 5) (91-2320-B-009-001- ) 21. H.-K. Tsai, J.-M. Yang, Y.-F. Tsai, and C-Y Kao, "An evolutionary approach for gene expression patterns," IEEE Transaction on Information Technology in Biomedicine, vol. 8, pp. 69-78, 2004. (IF: 1.436; Times Cited: 4) 22. H.-K. Tsai, J.-M. Yang, Y.-F. Tsai, and C-Y Kao, "An evolutionary algorithm for large traveling salesman problems," IEEE Transaction on Systems, Man, and Cybernetics, vol. 34, pp. 1718-1729, 2004. (IF: 1.353; Times Cited: 7) 23. H.-K. Tsai, J.-M. Yang, and C-Y Kao, "Issues of designing genetic algorithms for traveling salesman problems", vol. 8, pp. 689-697, Soft Computing, 2004. 24. J.-M. Yang*, T.-W. Shen, Y.-F. Chen, Y.-Y. Chiu, "An evolutionary approach with pharmacophore-based scoring functions for virtual database screening," Lecture Notes in Computer Science, vol. 3102, pp. 481-492, 2004. (91-2320-B-009-001- ) 25. Y.-C. Chen, J.-M Yang, C.-H. Tsai, C.-Y. Kao, "Comparative molecular binding energy analysis of HIV-1 protease inhibitors using genetic algorithm-based partial least squares method," Lecture Notes in Computer Science, vol. 3103, pp. 385-386, 2004. 26. C.-C. Chuang, C-Y Chen, J.-M. Yang, P.-C. Lyu, J.-K. Hwang, "The detection of protein structural similarity using disulfide-binding patterns," Proteins: Structure, Function, and Genetics, vol. 53, pp. 1-5, 2003. (IF: 3.354; Times Cited: 22) 27.
C.-S. Yu,
J.-Y. Wang, J.-M. Yang, P.-C. Lyu, C.-J. Lin, J.-K. Hwang, "Fine-grained
protein fold assignment by support vector machines using generalized 28. Y.-W. Chu* and J.-M. Yang*, "Finding regularity in various types of secondary protein structures," Journal of Information Science and Engineering, vol. 19, pp.943-952, 2003. (SCI) (90-2316-B-009-001- ) 29. E.-S. Lin, J.-M. Yang, and Y.-S. Yang, "Modeling the binding and inhibition mechanism of nucleotide and sulfotransferase using molecular docking," Journal of the Chinese Chemical Society, vol. 50, pp. 655-663, 2003. (IF:0.643; Times Cited: 2) (91-2320-B-009-001- ) 30. H.-K. Tsai, J.-M. Yang, Y.-F. Tsai, and C-Y Kao, "A heterogeneous selection genetic algorithm for traveling salesman problems," Engineering Optimization, pp. 297-311, 2003. (IF:0.571; Times Cited: 2) 31. J.-M. Yang*, "An evolutionary approach for molecular docking," Lecture Notes in Computer Science, vol. 2724, pp. 2372-2383, 2003. (91-2320-B-009-001- ) 32. J.-M. Yang*, C. H. Tsai, M.-J. Hwang*, H. K. Tsai, J. K. Hwang, and C.Y. Kao, "GEM: a Guassian evolutionary method for predicting protein side-chain conformations," Protein Science, vol. 11, no. 8, pp. 1897-1907, 2002. (SCI; Times Cited: 10) 33. J.-M. Yang*, C.-J. Lin, and C.-Y. Kao, "A robust evolutionary algorithm for global optimization," Engineering Optimization, vol. 34, no. 5, pp. 405-427, 2002. (SCI; Times Cited: 2) 34. J.-M. Yang* and C.-Y. Kao, "An efficient evolutionary algorithm for the thin-film synthesis of inhomogeneous optical coatings," Applied Optics, vol. 40, no. 19, pp. 3256-3267, 2001. (SCI; Times Cited: 4) 35. J.-M. Yang* and C.-Y. Kao, "A robust evolutionary algorithm for training neural networks," Neural Computing and Application, vol. 10, no. 3, pp. 214-230, 2001. (SCI; Times Cited: 10) 36. J.-M. Yang*, J.-T Horng, C.-J. Lin, and C.-Y. Kao, "Optical coating designs using an evolutionary algorithm," Evolutionary Computation, vol. 9, no.4, pp. 421-443, 2001. (SCI ; Times Cited: 5) 37. J.-M. Yang* and C.-Y. Kao, "An evolutionary algorithm for the synthesis of multilayer coatings at oblique light incidence," Journal of Lightwave Technology, vol. 19, no. 4, pp. 559-570, 2001. (SCI; Times Cited: 10) 38. J.-M. Yang* and C.-Y. Kao, "Flexible ligand docking using a robust evolutionary algorithm," Journal of Computational Chemistry, vol. 21, no. 11, pp. 988-998, 2000. (IF: 4.297;; Times Cited: 16) 39. J.-M. Yang* and C.-Y. Kao, "A Family competition evolutionary algorithm for automated docking of flexible ligands to Proteins," IEEE Transaction on Information Technology in Biomedicine, vol. 4, no. 3, pp. 225-237, 2000. (SCI; Times Cited: 4) 40. J.-M. Yang*, J.-T. Horng, and C.-Y. Kao, "A genetic algorithm with adaptive mutations and family competition for training neural networks," vol. 10, no.5, International Journal of Neural Systems, pp. 333-352, 2000. 41. J.-M. Yang* and C.-Y. Kao, "Integrating adaptive mutations and family competition into genetic algorithms as function optimizer," Soft Computing, vol. 4, no. 2, pp. 89-102, 2000
Conference Papers 1. K-C Hsu, Y-F Chen, and J-M Yang*, "Binding affinity analysis of protein-ligand complexes," 2nd International Conference on Bioinformatics and Biomedical Engineering, pp. 167-171, 2008. 2. J-W Huang, C-C Chen, and J-M Yang*, "Identifying critical positions and rules of antigenic drift for influenza A/H3N2 viruses," 2nd International Conference on Bioinformatics and Biomedical Engineering, pp. 249-252, 2008. 3. Y.-L. Chang, H.-K. Tsai, C.-Y. Kao and J.-M. Yang*, "Evolutionary conservation of DNA-contact residues in DNA-binding domains," International Multi-Symposiums on Computer and Computational Sciences (IMSCCS07), pp. 9-16, 2007. 4. J.-M. Yang*, L.-S. Chang, and K.-P. Liu, "ARPPI: A knowledge-based model for protein-protein interactions," Sixth International Conference on Bioinformatics (InCoB2007), 2007 5. Y.-C. Chen, H.-C. Chen and J.-M Yang*, "A 3D-domain annotated protein-protein interaction database," Genome Informatics, vol. 17, pp. 206-215, 2006. 6. Y.-Y. Chiu, J.-K. Hwang and J.-M. Yang, "GEMSCORE: A new empirical energy function for protein folding," IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2005), pp. 303-310, 2005. 7. J.-M. Yang and T.-W. Shen, "A pharmacophore-based evolutionary approach for screening estrogen receptor antagonists," Congress of Evolutionary Computation (CEC 2004), pp. 1028-1035, 2004. 8. H.-K. Tsai, J.-M. Yang, and C-Y Kao, "Applying genetic algorithms to finding the optimal gene order in displaying the microarray data," Proc. of the Genetic and Evolutionary Computation Conference (GECCO 2002), pp. 610-617, 2002. 9. H.-K. Tsai, J.-M. Yang, and C-Y Kao, "Solving traveling salesman problems by combining global and local search mechanisms," Congress of Evolutionary Computation (CEC 2002), pp. 1290-1295, 2002.
Posters 1. Y.-F. Chen, L.-J. Chang, J.-M. Yang*, "Integrating GEMDOCK with GEM-PLS and GEM-kNN for QSAR modeling of huAChE and AGHO," in 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria, 2007. 2. C.-H. Tung, T.-K. Yang, and J.-M. Yang*, "Structural Binding Pocket Clustering and Protein-Ligand Interaction Analysis for ATP-binding Proteins," in 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria, 2007. 3. Y.-S. Lo, Y.-S. Chang, and J.-M. Yang*, "New energy model for protein-protein interaction prediction," in 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria, 2007. 4. C-C. Chen, M.-H. Wu, C.-C. King, and J.-M. Yang, "Molecular phylogeny and genotypic change in envelope glycoprotein of dengue serotype 2 viruses in Taiwan and global comparison," in Second Asian Regional Dengue Research Network Meeting, Singapore, 2005. 5. C-C. Chen, M.-H. Wu, C.-C. King, and J.-M. Yang, "Molecular analysis of epidemic causing dengue 2 strains in Taiwan from 1981 to 2003," in Congress of the International Union of Microbiological societies, San Francisco, USA, 2005. 6. C-C. Chen, M.-H. Wu, C.-C. King, and J.-M. Yang, "Predicting antigenic variation and evolutionary trends of human influenza A/H3N2 viruses," The American Society for Virology, Pennsylvania State University, USA, 2005. 7. C-C. Chen, J.-M. Yang, M.-H. Wu, C.-K. Chow, and C.-C. King, "Global comparison of envelope proteins of dengue virus serotype 2 including Taiwan isolates over years," in First Asian Regional Dengue Research Network Meeting, Thailand, 2004. 8. C.-J. Chen, J.-M. Yang, and C.-Y. Kao, "A combinatorial method for protein loop prediction," in The Computational Systems Bioinformatics Conference (CSB 2004), 2004. 9. E.-S. Lin, J.-M. Yang, and Y.-S. Yang, "Modeling the Binding and Inhibition Mechanism of Nucleotide and Sulfotransferase Using Molecular Docking," in Worldwide Chinese Theoretical and Computational Chemistry Conference (WCTCC), 2002. 10. J-M Yang, K.-P. Liu , and F.-Z. Ting, "Molecular Recognition of the Inhibitors for HIV-1 protease by Flexible Docking," in Worldwide Chinese Theoretical and Computational Chemistry Conference (WCTCC), 2002. |
peptide coding
schemes and jury voting from multiple parameter sets," Proteins:
Structure, Function, and Genetics, vol. 50, pp. 531-536, 2003. (