PUBLICATIONS

 

In Chronological Order • By Subject

Data Mining and Machine Learning

  • Aaron Smalter, Jun Huan, and Gerald Lushington. A Graph Pattern Diffusion Kernel for Chemical Compound Classification. to appear in Proceedings of the 8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE'08), 2008. PDF
  • Hongliang Fei, Jun Huan, Structure Feature Selection for Chemical Compound Classification, to appear in Proceedings of the 8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE'08), 2008. PDF
  • Aaron Smalter, Jun Huan, and Gerald Lushington. GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification. to appear in Proceedings of the 8th Internation Workshop of Data Mining in Bioinformatics (BIOKDD'08), 2008. PDF
  • Jun Huan, Frequent Subgraph Mining, to appear in Encyclopedia of Database Systems, 2008.
  • Hongliang Fei, Jun Huan, Structure Feature Selection for Graph Classification, to appear in Proceedings of the  ACM 17th Conference on Information and Knowledge Management (CIKM), 2008. PDF
  • Aaron Smalter, Jun Huan, Gerald Lushington, Graph Wavelet Alignment Kernels for Drug Virtual Screening, to appear in Proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB), 2008. acceptance rate 30/135=22%, PDF
  • Aaron Smalter, Jun Huan, Gerald Lushington, Structure-based Pattern Mining For Chemical Compound Classification, to appear in Proceedings of the 6th Asia Pacific Bioinformatics Conference (APBC), 2008. PDF
  • Xiang Zhang, Wei Wang, Jun Huan, "On demand Phenotype Ranking through Subspace Clustering", in Proceedings of SIAM International Conference on Data Mining (SDM), 2007. PDF
  • David Williams, Jun Huan, Wei Wang, Graph Database Indexing Using Structured Graph Decomposition, in Proceedings of the 23rd IEEE International Conference on Data Engineering (ICDE), 2007. PDF
  • Jun Huan, "Graph Based Pattern Discovery in Protein Structures", Ph.D. Dissertation, Department of Computer Science, University of North Carolina, 2006
  • Jun Huan, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, Alex Tropsha, Wei Wang, "Distance-based Identification of Spatial Motifs in Proteins Using Constrained Frequent Subgraph Mining", in Proceeding of the IEEE Computational Systems Bioinformatics (CSB), 2006. PDF
  • Jun Huan, Wei Wang, and Jan Prins, "Protein Local Structure Comparison: Methods and Future Directions", in Advances in Computers by Chau-Wen Tseng (eds.), Elsevier, 2006.
  • Jun Huan, Deepak Bandyopadhyay, Wei Wang, Jack Snoeyink, Jan Prins, and Alex Tropsha. "Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs ", Journal of Computational Biology(JCB),  Vol. 12, No. 6: 657-671, 2005.  PDF
  • Jun Huan, Wei Wang, Jan Prins, and Jiong Yang. "SPIN: Mining Maximal Frequent Subgraphs from Graph Databases",  in Proceedings of the 10th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 581-586, 2004. PDF  Tech Report
  • Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, and Alex Tropsha. "Mining Family Specific Residue Packing Patterns from Protein Structure Graphs", in Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 308-315, 2004. PDF, Presentation  
  • Jun Huan, Wei Wang, Angliana Washington, Jan Prins, Ruchir Shah, and Alex Tropsha. "Accurate Classification of Protein Structural Families using Coherent Subgraph Analysis", in Proceedings of the Pacific Symposium on Biocomputing (PSB), pp. 411-422, 2004. PDF
  • Jun Huan, Wei Wang, and Jan Prins. "Efficient Mining of Frequent Subgraph in the Presence of Isomorphism", in Proceedings of the 3rd IEEE International Conference on Data Mining (ICDM), pp. 549-552, 2003. PDF, Tech Report Presentation

Chemical Genomics

  • Aaron Smalter, Jun Huan, and Gerald Lushington. A Graph Pattern Diffusion Kernel for Chemical Compound Classification. to appear in Proceedings of the 8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE'08), 2008. PDF
  • Aaron Smalter, Jun Huan, and Gerald Lushington. GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification. to appear in Proceedings of the 8th International Workshop of Data Mining in Bioinformatics (BIOKDD'08), 2008. PDF
  • Aaron Smalter, Jun Huan, Gerald Lushington, Graph Wavelet Alignment Kernels for Drug Virtual Screening, to appear in Proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB), 2008. acceptance rate 30/135=22%, PDF
  • Aaron Smalter, Jun Huan, Gerald Lushington, Structure-based Pattern Mining For Chemical Compound Classification, to appear in Proceedings of the 6th Asia Pacific Bioinformatics Conference (APBC), 2008. PDF

Functional Genomics

  • Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang, and Alexander Tropsha, Functional Neighbors: Relationships between Non-homologous Protein Families Inferred Using Family-Specific Fingerprints, to appear in Proceedings of the IEEE International Conference on Bioinformatics and  Biomedicine (BIBM'08), 2008. acceptance rate 38/156 = 24%,  PDF
  • Seak Fei Lei, Jun Huan, Towards Site-based Function Annotations for Protein Structures. to appear in Proceedings of the IEEE International Conference on Bioinformatics and  Biomedicine (BIBM'08), 2008. acceptance rate 38/156 = 24%, PDF,  Appendix
  • Xueyi Wang, Jun Huan, Jack Snoeyink,Wei Wang, Mining RNA Tertiary Motifs with Structure Graphs, to appear in Proceedings of the 19th International Conference on Scientific and Statistical Database Management (SSDBM), 2007.
  • Deepak Bandyopadhyay, Jun Huan, Jinze Liu, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha, "Structure-based Function Inference Using Protein Family-specific Fingerprints ", Journal of  Protein Science, Vol. 15, Page: 1537–1543. PubMed link
  • Jun Huan, Deepak Bandyopadhyay, Wei Wang, Jack Snoeyink, Jan Prins, and Alex Tropsha. "Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs ", Journal of Computational Biology(JCB),  Vol. 12, No. 6: 657-671, 2005.  PDF
  • Jun Huan, Deepak Bandyopadhyay, Jinze Liu, Jan Prins, Jack Snoeyink, Alex Tropsha, and Wei Wang. "Rapid Determination of Local Structural Features Common to a Set of Proteins ", Intelligent Systems for Molecular Biology (ISMB) (demo),  2005. PDF
  • Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, and Alex Tropsha. "Mining Family Specific Residue Packing Patterns from Protein Structure Graphs", in Proceedings of the 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pp. 308-315, 2004. PDF, Presentation 
  • Jun Huan, Wei Wang, Angliana Washington, Jan Prins, Ruchir Shah, and Alex Tropsha. "Accurate Classification of Protein Structural Families using Coherent Subgraph Analysis", in Proceedings of the Pacific Symposium on Biocomputing (PSB), pp. 411-422, 2004. PDF

Systems Biology
  • Xiang Zhang, Wei Wang, Jun Huan, "On demand Phenotype Ranking through Subspace Clustering", in Proceedings of SIAM International Conference on Data Mining (SDM), 2007. PDF
  • Jun Huan, Jan Prins, Wei Wang, and Todd Vision. "Reconstructing of Ancestral Gene Order after Segmental Duplication and Gene Loss", in Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB), pp. 484-485, 2003. PDF
  • Jingmei Liu, Yuan Yuan, Jun Huan & Zhiyuan Shen. "Inhibition of Breast and Brain Cancer Cell Growth by BCCIP, an Evolutionarily Conserved Nuclear Protein that Interacts with BRCA2", in Oncogene, Volume 20, Number 3. pp. 336-345, January 2001. PDF
  • Mark G. D'Souza, Jun Huan, Samantha Sutton, Margie Romine, and Natalia Maltsev, "PUMA2 -- An Environment for Comparative Analysis of Metabolic Subsystems and Automated Reconstruction of Metabolism of Microbial Consortia and Individual Organisms from Sequence Data" Technical Memorandum ANL/MCS-TM-240, December 1999. Link

Irregular Parallel Computation

  • Stephen Olivier, Jun Huan, Jinze Liu, Jan Prins, James Dinan, P Sadayappan and Chau-Wen Tseng. "UTS: An Unbalanced Tree Search Benchmark", in Proceedings of the 19th Intl. Workshop on Languages and Compilers for Parallel Computing (LCPC 2006). New Orleans, LA, November 2-4, 2006. PDF
  • K. Berlin, J. Huan, M. Jacob, G. Kochhar, J. Prins, W. Pugh, P. Sadayappan, J. Spacco, C.-W. Tseng, "Evaluating the Impact of Programming Language Features on the Performance of Parallel Applications on Cluster Architectures", in Proceedings of the 16th Intl. Workshop on Languages and Compilers for Parallel Computing (LCPC 2003), 2003 PDF
  • Jan Prins, Jun Huan, Bill Pugh, Chau-Wen Tseng, and P Sadayappan. "UPC Implementation of an Unbalanced Tree Search Benchmark", in Technical Reports produced by the Department of Computer Science at the University of North Carolina, Chapel Hill, 2003. PDF