Book and Ph.D. Dissertation

29 Shaobo Li and Jianjun Hu. Book: Genetic Programming and Creative Design of Mechatronic Systems China Machine Press. 2009 Abstract
28 J. Hu. Sustainable Evolutionary Algorithms and Scalable Evolutionary Synthesis of Dynamic Systems. PhD thesis, Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, 48823, USA, 2004 Click to download PDF File
Advisor: Erik Goodman

Journal Publications

27 J. Lin, A. Mondal, R. Liu and J. Hu. Minimalist Ensemble Algorithms for Genome-wide Protein Localization Prediction. BMC Bioinformatics, 13:157, 2012 Click to download PDF File
26 A. Mondal and J. Hu, Network Based Prediction of Protein Localization Using Diffusion Kernel.. Int. Journal of Data Mining and Bioinformatics. 2012 (in press) Click to download PDF File
25 R. Liu and J. Hu, Computational Prediction of Heme-Binding Residues by Exploiting Residue Interaction Network. PLoS ONE 6(10): e25560., 2011 Click to download PDF File
24 R. Liu and J. Hu, HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information., BMC Bioinformatics, 2011, 12:207 Click to download PDF File
23 E. Atilgan and J. Hu, Improving Protein Docking Using Sustainable Genetic Algorithms. International Journal of Computer Information Systems and Industrial Management (IJCISIM), Vol 3, 2011 Click to download PDF File
22 R. Liu and J. Hu, Prediction of discontinuous B-cell epitopes using logistic regression and structural information”, Journal of Proteomics & Bioinformatics, 4: 010-015, 2011 Click to download PDF File
21 J. Hu and J. Xu, Density based Pruning for Identification of Differentially Expressed Genes., BMC Genomics, 11(2):S3, 2010 Click to download PDF File
20 J. Hu and Fan Zhang, "BayesMotif: De novo Protein Sorting Motif Discovery from Impure Datasets. BMC Bioinformatics, 11(Suppl 1):S66, 2010 Click to download PDF File
19 H. Chen, G. Pimienta, Y. Gu, X. Sun, J. Hu, M. K. Chaerkady, M. Gucek, R. Cole, S. Sukumar, A. Pandey, Proteomic characterization of Her2/neu-overexpressing breast cancer cells. PROTEOMICS, 10, 3800–3810, 2010 Click to download PDF File
18 HO. Gonzalez, J. Hu, KM. Gaworecki, JA. Roling, WS. Baldwin, Gardea-Torresdey JL, Bain LJ. Dose-responsive gene expression changes in juvenile and adult mummichogs (Fundulus heteroclitus) after arsenic exposure, Mar Environ Res, 70(2): 133-141. 2010 Click to download PDF File
17 H. Luo, R. Benner, R. A. Long, J. Hu, "Subcellular Localization of Marine Bacterial Alkaline Phosphatases " Proceeding of National Academy of Science (PNAS), November 19, 2009 Click to download PDF File
16 Liu CC, Hu J, Kalakrishnan M, Huang H, Zhou XJ " Integrative Disease Classification Based on Cross-platform Microarray Data. ", BMC Bioinformatics. 2009. 10(Suppl 1):S25 Click to download PDF File
15 J. Hu, E. D. Goodman, and R. C. Rosenberg, " Automated Synthesis of Mechanical Vibration Absorbers Using Genetic Programming", Journal of Artificial Intelligence for Engineering Design, Analysis and Manufacturing. 22(3), 2008 , Special Issue on Genetic programming for human-competitive design Click to download PDF File
14 J. Hu, Haifeng Li, Michael S Waterman, and Xianghong Jasmine Zhou. Integrative missing value estimation for microarray data. BMC Bioinformatics. 7: 449., 2006. Click to download PDF File
13 J. Hu, Yifeng David Yang and Daisuke Kihara, "EMD: an Ensemble Algorithm for discovering regulatory motifs in DNA sequences", BMC Bioinformatics, 7:342. 2006. Click to download PDF File
12 J. Hu, Bin Li, and Daisuke Kihara, "Limitations and Potentials of Current Motif Discovery Algorithms", Nucleic Acid Research, 33: 4899-4913, 2005Click to download PDF File
11 Fei Pan, Kiran Kamath, Kangyu Zhang, Sudip Pulapura, Avinash Achar, Juan Nunez-Iglesias, Yu Huang, Xifeng Yan, Jiawei Han, Haiyan Hu, Min Xu, J. Hu, Xianghong Jasmine Zhou. K. Kamath et. al. Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data. Bioinformatics, 22: 1665-1667, 2006. Click to download PDF File
10 S. Li, X. Chen and J. Hu. Study on Sustainable Evolutionary Algorithm Based on Hierarchical Search. China Mechanical Engineering (Chinese), 7(11), 2006.
8 J. Hu, E. Goodman, K.Seo, Z. Fan, R. Rosenberg, "The Hierarchical Fair Competition (HFC) Framework for Sustainable Evolutionary Algorithms", Evolutionary Computation, 13 (2), MIT Press, 2005. Click to download PDF File
7 J. Hu, E. Goodman, R. Rosenberg, "Topologically Open-Ended Synthesis of Dynamic Systems with High Robustness Using Genetic Programming: a Case Study of Analog Filter Synthesis", IEEE Transaction on Evolutionary Computation, IEEE Press, 2005. (accepted)
6 Z. Fan, K. Seo, J. Hu, E. Goodman, R. Rosenberg, "A Novel Evolutionary Engineering Design Approach for Mixed-Domain Systems," Journal of Engineering Optimization, Volume 36, Number 2, 2004. Click to download PDF File
5 K. Seo, Z. Fan, J. Hu, E. D. Goodman, and R. C. Rosenberg, "Toward an Automated Design Method for Multi-Domain Dynamic Systems Using Bond Graphs and Genetic Programming," Mechatronics , 13, (8-9), pp. 851-885, 2003.Click to download PDF File
4 K. Seo, J. Hu, Z. Fan, E. D. Goodman, and R. C. Rosenberg. Automated Design Approaches for Multi-Domain Dynamic Systems Using Bond Graphs and Genetic Programming," The International Journal of Computers, Systems and Signals, vol.3, no.1, pp.55-70, 2002. Click to download PDF File
3 S. Li, J. Hu, Q. Xie and H. Zhang. Automated Design of Mechtronic Systems based on Genetic Programming and Bond Graphs. Journal of System Simulation (Chinese), 14 (11): 1513-1516, 2002
2 J. Hu, Shuchun Wang, "An Overview of Computational Intelligence Solutions to Intelligent Manufacturing Problems", Journal of China Mechanical Engineering (Chinese). No.1., 1999.
1 J. Hu, Zhongfu. Zhang, "Weight Inducement and Hierarchical Training Algorithm of BP Neural Network", Journal of Computer Science (Chinese), No. 1, 1998.

Book Chapters

6 J. Hu, Zhun Fan, Jiachuan Wang, Shaobo Li, Kisung Seo, Xiangdong Peng, Janis Terpenny, Ronald Rosenberg, and Erik Goodman, GPBG: A Framework for Evolutionary Design of Multi-domain Engineering Systems Using Genetic Programming and Bond Graphs”. In Evolution by Design – Advances in Evolutionary Design. P. F. Hingston et. al. (ed.) Springer publisher, 2008. Click to download PDF File
5 J. Hu, S. Li & E. Goodman. Evolutionary Robust Design of Analog Filters using Genetic Programming,” in Evolutionary Computation in Dynamic and Uncertain Environments, Kacprzyk, J. (ed.), Springer, pp. 479-496, 2007
4 J. Hu, E. Goodman, “Domain Specificity of Genetic Programming based Automated Synthesis: a Case Study with Synthesis of Mechanical Vibration Absorbers”, in Genetic Programming Theory and Practice. Rick Riolo and Bill Worzel (eds.). Kluwer Publishers, Boston, MA. 2005.
3 J. Hu, E. Goodman. Evolving robust dynamic systems with genetic programming. In Genetic Programming Theory and Practice. Rick Riolo and Bill Worzel (eds.). Kluwer Publishers, Boston, MA. 2004.
2 J. Hu, K. Seo, E. Goodman, R. Rosenberg. Toward efficient topological synthesis of dynamic systems using bond graphs and genetic programming. Nadia Nedjah. (eds). Evolutionary Machine Design: Methodology and Applications. Nova Science Publishers, NY, USA, 2004.
1 J. Hu, E. Goodman and K. Seo. Continuous Hierarchical Fair Competition Model for Sustainable Innovation in Genetic programming. In Genetic Programming Theory and Practice. Rick Riolo and Bill Worzel (eds.). Kluwer Publishers, Boston, MA. 2003.

Conference Publications

20 A. Mondal and J. Hu, "Protein Localization by Integrating Multiple Protein Correlation Networks", Proceeding of 2012 International Conference on Bioinformatics and Computational Biology (BIOCOMP12), 2012 Click to download PDF File
19 A. Mondal and J. Hu, Network Based subcellular prediction for multi-label proteins”. The 4th Workshop on Biomolecular Network Analysis (IWBNA 2011) Click to download PDF File
18 A. Mondal and J. Hu, "NetLoc: Network Based Protein Localization Prediction Using Protein-Protein Interaction and Co-expression Networks", Proceeding of IEEE International Conference on Bioinformatics & Biomedicine (BIBM2010) Click to download PDF File
17 E. Atilgan and J. Hu, Efficient Protein-Ligand Docking Using Sustainable Evolutionary Algorithms, Proceeding of the 10th Int. Conference on hybrid intelligence (HIS2010), Atlanta, GA. USA, 2010 Click to download PDF File
16 F. Zhang and J. Hu, Bioinformatics Analysis of Physichemical Properties of Protein sorting Signals, Lecture Notes in Computer Science. Bioinformatics and Computational Biology BiCoB2010. Springer Berlin / Heidelberg, 2010 Click to download PDF File
15 F. Zhang and J. Hu, "Bayesian Classifier for Anchored Protein Sorting Discovery", Proceeding of 2009 IEEE International Conference on Bioinformatics & Biomedicine (BIBM09: Nov1-4 2009, USA). Click to download PDF File
14 J. Xu and J. Hu, "Improved Identification of Differentially Expressed Genes Using Pareto Gene Pruning", Proceeding of 2009 International Conference on Bioinformatics and Computational Biology (BIOCOMP'09: July 13-16, 2009, USA) Click to download PDF File
13 J. Hu, F. Zhang, " Improving Protein Localization Prediction Using Amino Acid Group Based Physichemical Encoding", 1st int. conf. Bioinformatics and Computational Biology (BICoB2009) Click to download PDF File
12 J. Hu, X. Zhong, E. Goodman, “Open-ended Robust Design of Analog filters Using Genetic Programming”, Proc. Genetic and Evolutionary Computation Conference. (Best paper nominee), 2005 Click to download PDF File
11 J. Hu, E. Goodman, “Robust and Efficient Genetic Algorithms with Hierarchical Niching and Sustainable Evolutionary Computation Model”, Proc.Genetic and Evolutionary Computation Conference.2004 Click to download PDF File
10 J. Hu, E. Goodman, “Wireless Access Point Configuration by Genetic Programming”, Proc. IEEE Congress on Evolutionary Computation (CEC) 2004. Click to download PDF File
9 J. Hu, E. Goodman, and R. Rosenberg, “Topological search in automated mechatronic system synthesis using bond graphs and genetic programming”, Proc. of American Control Conference (ACC), 2004. Click to download PDF File
8 J. Hu, K. Seo, Z. Fan, R. Rosenberg, and E. Goodman, " HEMO: A Sustainable Multi-Objective Evolutionary Optimization Framework", Proc. 2003 Genetic and Evolutionary Computation Conference, Chicago, Springer, Lecture Notes in Computer Science, July, pp. 1029-1040, 2003 Click to download PDF File
7 Z. Fan, K. Seo, J. Hu, R. Rosenberg, and E. Goodman, " System-Level Synthesis of MEMS via Genetic Programming and Bond Graphs", Proc. 2003 Genetic and Evolutionary Computation Conference, Chicago, Springer, Lecture Notes in Computer Science, July, pp. 2058-2071, 2003. Click to download PDF File
6 K. Seo, Z. Fan, J. Hu, E. Goodman, and R. Rosenberg, "Dense and Switched Modular Primitives for Bond Graph Model Design," Proc. 2003 Genetic and Evolutionary Computation Conference, Chicago, Springer, Lecture Notes in Computer Science, July, pp. 1764-1775., 2003 Click to download PDF File
5 J. Hu, E. D. Goodman, K. Seo, M. Pei, "Adaptive Hierarchical Fair Competition (AHFC) Model for Parallel Evolutionary Algorithms," Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2002, New York, July, pp. 772-779., 2002. Click to download PDF File
4 J. Hu, K. Seo, S. Li, Z. Fan, R. C. Rosenberg, E. D. Goodman, "Structure Fitness Sharing (SFS) for Evolutionary Design by Genetic Programming," Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2002, New York, pp. 780-787. , 2002. Click to download PDF File
3 Z. Fan, K. Seo, R. C. Rosenberg, J. Hu, E. D. Goodman, "Exploring Multiple Design Topologies using Genetic Programming and Bond Graphs", Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2002, New York, July, pp. 1073-1080, 2002 Click to download PDF File
2 J. Hu, E. D. Goodman, "Hierarchical Fair Competition Model for Parallel Evolutionary Algorithms," Proceedings, Congress on Evolutionary Computation, CEC 2002, IEEE World Congress on Computational Intelligence, Honolulu, Hawaii, May, 2002.Click to download PDF File
1 Z. Fan, J. Hu, K. Seo, E. D. Goodman, R. C. Rosenberg, and B. Zhang, "Bond Graph Representation and GP for Automated Analog Filter Design," 2001 Genetic and Evolutionary Computation Conference Late-Breaking Papers, E. Goodman, ed., ISGEC Press, San Francisco, pp. 81-86., 2001. Click to download PDF File

Workshop Contributions

4 J. Hu, E. D. Goodman, K. Seo, Z. Fan, R. C. Rosenberg, "HFC: A Continuing EA Framework for Scalable Evolutionary Synthesis", Proceedings of the 2003 AAAI Spring Symposium - Computational Synthesis: From Basic Building Blocks to High Level Functionality, Stanford, California, March, 24-26, pp. 106-113, 2003
3 Z. Fan, K. Seo, R. C. Rosenberg, J. Hu, E. D. Goodman, "Computational Synthesis of Multi-Domain Systems", Proceedings of the 2003 AAAI Spring Symposium - Computational Synthesis: From Basic Building Blocks to High Level Functionality, Stanford, California, March, 24-26, pp. 59-66, 2003
2 E. D. Goodman, K. Seo, Z. Fan, J. Hu, R. C. Rosenberg, "Automated Design of Mechatronic Systems: Novel Search Methods and Modular Primitives to Enable Real-World Applications," 2003 NSF Design, Service and Manufacturing Grantees and Research Conference, January 6-9, Birmingham, Alabama, 2003
1 E. D. Goodman, K. Seo, R. C. Rosenberg, Z. Fan, J. Hu, and B. Zhang, "Automated Design Methodology for Mechatronic Systems Using Bond Graphs and Genetic Programming," 2002 NSF Design, Service and Manufacturing Grantees and Research Conference, January 7-10, San Juan, Puerto Rico, 2002