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.

CALL FOR PAPER: CSSB2013 First International Workshop on Computational Synthesis of Systems from Building Blocks

First International Workshop on Computational Synthesis of Systems from Building Blocks (CSSB2013) will be held at GECCO 2013, July 6, 2013, Amsterdam, Netherland visit CSSB2013 page
Automated computational synthesis of circuit systems, mechatronic systems, control systems, optical systems, antennas, materials, and other structures by evolutionary algorithms such as genetic programming have attracted significant interest in the past decades. There is a core common element to these problems: a set of building blocks need to be selected, tuned and assembled into a system with a particular target behavior. Candidate systems are evaluated by a simulator such as Pspice, Matlab, Dymola, Modelica, NetSim, Ansys, or VASP. This workshop invites leading researchers and engineers interested in computational synthesis of systems to discuss realizing real-world applications.

Teaching

Spring 2013 Pattern Recognition (CSCE768)
TTH 11:00AM- 12:15PM, SWGN 2A22

Research Interests

• Bioinformatics and Functional Genomics: protein sorting signal analysis, protein binding residue gene expression regulation, DNA motif analysis, Microarray analysis
• Evolutionary Computation, Machine Learning, and Data Mining
• Computational material discovery, Computational design Synthesis, 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).

Hometown: I came from Hunan Yueyang, China. See one picture or listen to one piece of classic china music Love of Yellow River .

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

1

S. Li, J. Hu, Genetic Programming and Creative Design of Mechatronic Systems. China Machine Press. 2009

2

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. Advisor: Erik Goodman

1

J. Lin, A. Mondal, R. Liu and J. Hu. Minimalist Ensemble Algorithms for Genome-wide Protein Localization Prediction. BMC Bioinformatics, 13:157, 2012

2

A. Mondal and J. Hu, Network Based Prediction of Protein Localization Using Diffusion Kernel”. Int. Journal of Data Mining and Bioinformatics. 2012 (in press)

3

R. Liu and J. Hu, Computational Prediction of Heme-Binding Residues by Exploiting Residue Interaction Network”. PLoS ONE 6(10): e25560., 2011

4

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

5

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

6

J. Hu, Haifeng Li, Michael S Waterman, and Xianghong Jasmine Zhou. Integrative missing value estimation for microarray data. BMC Bioinformatics. 7: 449., 2006.

7

J. Hu, Yifeng David Yang and Daisuke Kihara, "EMD: an Ensemble Algorithm for discovering regulatory motifs in DNA sequences", BMC Bioinformatics, 7:342. 2006.

8

J. Hu, Bin Li, and Daisuke Kihara, "Limitations and Potentials of Current Motif Discovery Algorithms", Nucleic Acid Research, 33: 4899-4913, 2005

9

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

10

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.

1

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.

2

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

3

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, 2006

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.

5

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.

6

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

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

2

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)

3

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).

4

J. Hu and F. Zhang (2009), Improving Protein Localization Prediction Using Amino Acid Group Based Physichemical Encoding”. Lecture Notes in Computer Science. Bioinformatics and Computational Biology BiCoB2009. 5462/2009. Springer Berlin / Heidelberg

5

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

6

J. Hu, E. Goodman, “Robust and Efficient Genetic Algorithms with Hierarchical Niching and Sustainable Evolutionary Computation Model”, Proc.Genetic and Evolutionary Computation Conference.2004

7

J. Hu, E. Goodman, “Wireless Access Point Configuration by Genetic Programming”, Proc. IEEE Congress on Evolutionary Computation (CEC) 2004.

8

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.

9

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