Hongwei Wu, Ph.D.
Computational biology/bioinformatics, particularly in comparative genomic analysis and computational systems biology (modeling, estimating, simulating and predicting biological networks);
Computational intelligence theories and applications to computational biology/bioinformatics, pattern recognition and signal processing.
Ph.D. Electrical Engineering, University of Southern California, 2004.
- Dissertation: Rule-Based Systems for Data Processing
- Advisor: Dr. Jerry M. Mendel
M.S. Electrical Engineering, University of Southern California, 2002.
M.Eng. Pattern Recognition and Intelligent Systems, Department of Automation, Tsinghua University, Beijing, China, 1999.
B.Eng. Automatic Control, Department of Automation, Tsinghua University, Beijing, China, 1997.
Assistant Professor, School of Electrical and Computer Engineering, Georgia Institute of Technology, 2007 - present.
Post-doctoral Research Associate, Computational Biology Institute, Oak Ridge National Laboratory; and Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, University of Georgia, 2004 - 2007.
Research and Teaching Assistant, Department of Electrical Engineering, University of Southern California, 1999 - 2004.
Research and Teaching Assistant, Department of Automation, Tsinghua University, Beijing, China, 1995 - 1999.
Computational Biology and Bioinformatics
Hongwei Wu, "PCA-based linear combinations of k-mer freuencies for metagenomic DNA fragment binning," accepted by 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'08).
Hongwei Wu, F. Mao, V. Olman, Y. Xu, "On Application of Directons to Functional Classification of Genes in Prokaryotes," Computational Biology and Chemistry, vol. 32, pp. 176 - 184, 2008.
Hongwei Wu, F. Mao, V. Olman, Y. Xu, "Hierarchical Classification of Genes for Prokaryotic Genomes: from a Methodological Point of View," Proceedings of the Third International Symposium on Bioinformatics Research and Applications (ISBRA 2007), pp. 551 - 563, Atlanta, GA, 2007.
Hongwei Wu, F. Mao, V. Olman, Y. Xu, "Hierarchical Classification of Functionally Equivalent Genes in Prokaryotes," Nucleic Acids Research, 35(7):2125-2140, 2007.
F. Mao, Hongwei Wu, V. Olman, Y. Xu, "HCG: A Database for Hierarchical Classification of Functionally Equivalent Genes in Prokaryotes," submitted, 2006.
V. Olman, F. Mao, Hongwei Wu, Y. Xu, "A Parallel Clustering Algorithm for Very Large Data Sets," accepted by IEEE/ACM Transaction on Computational Biology and Bioinformatics, 2007.
Hongwei Wu, Z. Su, F. Mao, V. Olman, Y. Xu, "Prediction of Functional Modules through Comparative Genome Analysis and Application of Gene Ontology," Nucleic Acids Research, 33:2822-2837, 2005.
Hongwei Wu, F. Mao, V. Olman, Y. Xu, "Accurate Prediction of Orthologous Gene Groups in Microbes," Proceedings of the IEEE Computational Systems Bioinformatics Conference (CSB 2005), pp. 73 - 79, 2005.
Hongwei Wu, F. Mao, Z. Su, V. Olman, Y. Xu, "Prediction of Functional Modules Based on Gene Distributions in Microbial Genomes," Genome Informatics, vol. 16, pp. 247-259, 2005. [supplementary materials]
D. Che, G. Li, F. Mao, Hongwei Wu, and Y. Xu, "Detecting Uber-Operons in Microbial Genomes," Nucleic Acids Research, 34:2418-2427, 2006.
Z. Su, F. Mao, D. Phuongan, Hongwei Wu, V. Olman, P. Ian, P. Brian, and Y. Xu, "Computational Inference and Experimental Validation of Nitrogen Assimilation Regulatory Networks in Cyanobacterium Synechococcus sp. WH8102," Nucleic Acids Research, 34:1050-1065, 2006.
Signal Processing and Pattern Recognition
Hongwei Wu and J. M. Mendel, "Classification of Battlefield Ground Vehicles Using Acoustic Features and Fuzzy Logic Rule-Based Classifiers," IEEE Transactions on Fuzzy Systems (special issue on Extensions to Type-1 Fuzzy Sets), vol. 15, no. 1, pp. 56 -- 72, 2007.
Hongwei Wu and J. M. Mendel, "Multi-Category Classification of Ground Vehicles Based on the Acoustic Data of Multiple Terrains Using Fuzzy Logic Rule-Based Classifiers," in Unattended Ground Sensor Technologies and Applications VII, edited by Edward M. Carapezza, Proc. of SPIE, vol. 5796, pp. 28-39, 2005.
Hongwei Wu and J. M. Mendel, "Multicategory Classification of Ground Vehicles Based on Their Acoustic Emissions," in Unattended/Unmanned Ground, Ocean, and Air Sensor Technologies and Applications VI, edited by Edward M. Carapezza, Proc. of SPIE, vol. 5417, pp. 31-42, 2004.
Hongwei Wu and J. M. Mendel, "Quantitative Analysis of Spatio-Temporal Decision Fusion Based on the Majority Voting Technique," in Multisensor, Multisource Information Fusion: Architectures, Algorithms, and Applications 2004, edited by Belur V. Dasarathy, Proc. of SPIE, vol. 5434, pp. 13-24, 2004.
Hongwei Wu and J. M. Mendel, "Classifier Designs for Binary Classifications of Ground Vehicles," in Unattended Ground Sensor Technologies and Applications V, edited by Edward M. Carapezza, Proc. of SPIE, vol. 5090, pp. 122-133, 2003.
Hongwei Wu and J. M. Mendel, "Classification of Ground Vehicles from Acoustic Data Using Fuzzy Logic Rule-Based Classifiers: Early Results," in Unattended Ground Sensor Technologies and Applications IV, edited by Edward M. Carapezza, Proc. of SPIE, vol. 4743, pp. 62-72, 2002.
Computational Intelligence
J. M. Mendel and Hongwei Wu, "Type-2 Fuzzistics for Non-Symmetric Interval Type-2 Fuzzy Sets: Forward Problems," accepted by IEEE Transactions on Fuzzy Systems, 2006.
J. M. Mendel and Hongwei Wu, "New Results about the Centroid of an Interval Type-2 Fuzzy Set, Including the Centroid of a Fuzzy Granule," Information Sciences , vol. 17, pp. 360-377, 2007.
J. M. Mendel and Hongwei Wu , "Type-2 Fuzzistics for Symmetric Interval Type-2 Fuzzy Sets: Part I, Forward Problems," IEEE Transactions on Fuzzy Systems, vol. 14, no. 6, pp. 781-792, 2006.
J. M. Mendel and Hongwei Wu , "Type-2 Fuzzistics for Symmetric Interval Type-2 Fuzzy Sets: Part 2, Inverse Problems, "IEEE Transactions on Fuzzy Systems, vol. 15, no. 2, pp. 301-308, 2007.
Hongwei Wu and J. M. Mendel, "On Choosing Models for Linguistic Connector Words for Mamdani Fuzzy Logic Systems," IEEE Transactions on Fuzzy Systems, vol. 12, no. 1, pp. 29-44, 2004.
Hongwei Wu and J. M. Mendel, "Uncertainty Bounds and their Use in the Design of Interval Type-2 Fuzzy Logic Systems," IEEE Transactions on Fuzzy Systems, vol. 10, no. 5, pp. 622-639, 2002.
Hongwei Wu and J. M. Mendel, "Antecedent Connector Word Models for Interval Type-2 Fuzzy Logic Systems," Proc. of the IEEE International Conference on Fuzzy Systems (FUZZ IEEE 2004), vol. 2, pp. 1099¨C1104, 2004.
J. M. Mendel and Hongwei Wu , "Uncertainty versus Choice in Rule-Based Fuzzy Logic Systems," Proc. of the 2002 IEEE International Conference on Fuzzy Systems (FUZZ IEEE 2002), vol. 2, pp. 1336-1341, 2002.
Program Committee Member the 4th International Symposium on Bioinformatics Research and Applications (ISBRA2008) .
Program Committee Member and Session Chair (Gene networks, pathways, and protein domain interactions) for the 2007 International Symposium on Bioinformatics Research and Applications (ISBRA2007) .
Co-organizer for the workshop on Systems Biology for Microbial Genomes at the 2007 Life Science Society Computational Systems Bioinformatics Conference (CSB 2007).
Program Committee Member for the 2007 IEEE International Conference on Granular Computing (GrC 2007).
Program Committee Member for the IEEE 7-th International Symposium on Bioinformatics and BioEngineering (BIBE07).
Co-session chair (Metagenome Informatics) for the 39th Symposium on the Interface: Computing Science and Statistics (Theme: Systems Biology) (Interface07).
Tutorials Chair for the 2007 International Joint Conference on Neural Networks (IJCNN 2007).
Co-Organizer for the Workshop on Comparative Genome Analyses of Bacterial Genomes and Applications at the 2006 Life Science Society Computational Systems Bioinformatics Conference (CSB2006).
Program Committee Member for the 2006 IEEE International Conference on Granular Computing.
Committee Member for Women in Computational Intelligence of the IEEE Computational Intelligence Society
Reviewer
WCCI2008, ECCB05, CSB2005, ISMB2005, ICBA'04, IEEE Transactions on Fuzzy Systems, IEEE Transactions on Systems, Man and Cybernetics - Part B, Signal Processing, Ecological Modelling, International Journal of Robotics and Automation, International Journal of Approximate Reasoning , Information Sciences, Applied Mathematics Letters, Control and Cybernetics, EURASIP Journal on Wireless Communications and Networking, International Journal of Sensor Networks (IJSNET) ,IEEE FUZZ 2002, 2003, 2005, and IEEE INFOCOM 2004.
Best Research Paper Award, Department of Electrical Engineering, University of Southern California, 2002.
Graduate with Honor for M.Eng., Tsinghua University, Beijing, China, 1999.
Rockwell-Tshinghua Scholarship, Department of Automation, Tshinghua University, Beijing, China, 1998.
Excellent Science and Technology Student Scholarship, Beijing Municipal Education Commission, China, 1995.
Student Scholarship, First Prize, Department of Automation, Beijing, Tsinghua University, China, 1993-1996.
Supplementary Materials for "PCA-based Linear Combinations of Oligonucleotide Frequencies for Metagenomic DNA Fragment Binning": Table S1 and Table S2
Files for Downloading: NC_000913.redundance_removed.integer
C/C++ Program and Sample Data Files to Calculate the Gene Ontology Distance between Genes: GOProgram.tar
Hierarchical Classification Results for 224 Prokaryotic Genomes: HCG_05092006.tar.gz