Jianjun Hu

Assistant Professor

Department of Computer Science and Engineering
University of South Carolina
Columbia, SC 29208
Office: 3A66 Swearingen Engineering Center
Phone: 803-777-7304  
   Fax: 803-777-3767
 Email: jianjunh_AT_cse.sc.edu

Office hours:TBD

News
I was recently awarded NSF CAREER Award for "Computational Analysis and Prediction of Genome-Wide Protein Targeting Signals and Localization". This project starts from August 2009 and lasts five years. Detailed information can be found at NSF Award link

I am looking for highly motivated Ph.D. students with RA assistantship to join my lab and work on projects in bioinformatics,data mining or machine learning. Background of biology and data mining or machine learning is preferred but not required. You are expected to have good programming skills and teamwork spirit.

Teaching

Fall 2009 Data Structure and Algorithmis (CSCE350)
TH 2:00PM- 3:15PM, SWGN 2A21

Spring 2009 course: Parallel Computing (CSCE569)
MW 11:15PM- 12:05PM, SWGN 2A21

Fall 2008 course: Data mining principles and applications (CSCE822)
MW 4:00PM- 5:15PM, SWGN 2A21

Spring 2008 course: Algorithms for Bioinformatics (CSCE555)
MW 4:00PM- 5:15PM, SWGN 2A21

Fall 2007 course: Data mining principles and applications (CSCE822)
MW 4:00PM- 5:15PM, SWGN 2A21

Research Interests
  • Bioinformatics: gene expression regulation, DNA motif analysis, Microarray analysis
  • Integrative Functional Genomics
  • Evolutionary Computation and Computational Synthesis
  • Machine Learning, Data Mining, and Open-ended Modeling and Knowledge Discovery

For more information, pls visit my lab's homepage here: Machine Learning and Evolution Group (MLEG)

Bio: I joined CSE department of the University of South Carolina in August 2007. I am now working on integrative functional genomics and especially integrative analysis of microarray data. I am also interested in motif discovery for understanding gene expression mechanisms involved in diseases. I got my Ph.D. in Computer Science in the area of machine learning and particularly evolutionary computation at the Genetic Algorithm Research and Application Group (GARAGe) of Michigan State University. My dissertation focuses on sustainable evolutionary computation algorithms and automated computational synthesis. I have worked on the DNA motif discovery problem as Postdoc at Kihara Bioinformatics Lab, Purdue University and microarray analysis at the Computational Molecular Biology Division at the University of Southern California (another USC).

Education

Postdoc University of Southern California, Computational Molecular Biology 09/05 - 06/07
Postdoc Purdue University, Biological Science 09/04 - 08/05
Ph.D.  Michigan State University, Computer Science 08/00 - 07/04
M.S.  Wuhan University of Technology, China, Mechanical Engineering 07/95 - 04/98
B.S.  Wuhan University of Technology, China, Mechanical Engineering 09/91 - 07/95

Selected Publications [Complete List]

Journal Publications

0 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
1 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
2 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
3 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
4 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
5 J. Hu, E. D. Goodman, and R. C. Rosenberg, " Automated Synthesis of Mechanical Vibration Absorbers Using Genetic Programming", Computer-Aided Design , Special Issue on human-competitive evolutionary design, 2005 (in print)
6 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

Book Chapters

1 J. Hu, Z. Fan, J. Wang, X. Peng, K. Seo, J. Terpenny, and E. Goodman. GPBG: A Framework for Evolutionary Synthesis of Multi-domain Engineering Systems. Eds. Kalyanmoy Deb, (in press), 2006
2 J. Hu, S. Li and E. Goodman. Evolutionary Robust Design of Analog Filters using Genetic Programming. In Evolutionary Computation in Dynamic and Uncertain Environments, Springer Series on Studies in Computational Intelligence. 2006. (in press)
3 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.

Conference Publications

1 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
2 J. Hu, E. Goodman, “Robust and Efficient Genetic Algorithms with Hierarchical Niching and Sustainable Evolutionary Computation Model”, Proc.Genetic and Evolutionary Computation Conference.2004
3 J. Hu, E. Goodman, “Wireless Access Point Configuration by Genetic Programming”, Proc. IEEE Congress on Evolutionary Computation (CEC) 2004.
4 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.
5 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