PUBLICATIONS

In Chronological Order • By Subject

Jounal Papers & Book Chapters:

  1. Aaron Smalter, Jun Huan, and Gerald Lushington, GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009
  2. Deepak Bandyopadhyay, Jun Huan, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha, Identification of Family-Specific Residue Packing Motifs and their use for Structure-Based Protein Function Prediction, I. Method Development, Journal of Computer-Aided Molecular Design, 2009 
  3. Deepak Bandyopadhyay, Jun Huan, Jan Prins, Jack Snoeyink, Wei Wang, Alexander Tropsha, Identification of Family-Specific Residue Packing Motifs and their use for Structure-Based Protein Function Prediction: II. Case Studies and Applications, Journal of Computer-Aided Molecular Design, 2009
  4. Seak Fei Lei and Jun Huan, Towards Site-based Protein Functional Annotations, the International Journal of Data Mining in Bioinformatics, 2009
  5. Aaron Smalter, Jun Huan, Gerald Lushington, Graph Wavelet Alignment Kernels for Drug Virtual Screening, Journal of Bioinformatics and Computational Biology, Vol. 7 (3), pp. 473-497, 2009
  6. Yi Jia, Jun Huan, Vincent Buhr, Jintao Zhang, and Leonidas N. Carayannopoulos, "Towards Comprehensive Structural Motif Mining for Better Fold Annotation in the “Twilight Zone” of Sequence Dissimilarity", BMC Bioinformatics, Vol. 10 (Suppl 1): S46, 2009  PDF
  7. Jun Huan, Frequent Subgraph Mining, to appear in Encyclopedia of Database Systems, 2008
  8. 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.
  9. 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. 2006. PubMed link
  10. Jun Huan, Deepak Bandyopadhyay, Wei Wang, Jack Snoeyink, Jan Prins, and Alexander 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
  11. 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

Conference Papers:

2009

  1. Aaron Smalter, Jun Huan, Gerald Lushington, Feature Selection in the Feature Tensor Product Space, in Proceedings of the 9th IEEE International Conference on Data Mining (ICDM'09), 2009. short paper, acceptance rate 18%
  2. Hongliang Fei, Jun Huan, L2 Norm Regularized Feature Kernel Regression For Graph Data, in Proceedings of the  ACM 18th Conference on Information and Knowledge Management (CIKM'09), 2009. acceptance rate 123/847=15%, Best Paper Runner-up (6/123 accepted papers)
  3. Brian Quanz, Jun Huan, Large Margin Transductive Transfer Learning, in Proceedings of the  ACM 18th Conference on Information and Knowledge Management (CIKM'09), 2009. acceptance rate 123/847=15%
  4. Xiaohong Wang, Jun Huan, Aaron Smalter, Gerald Lushington, Application of Kernel Functions for Accurate Similarity Search in Large Chemical Databases, in Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine (BIBM'09), 2009. regular paper, acceptance rate 44/233 = 19%.
  5. Yi Jia, Jun Huan, The Analysis of Arabidopsis Thaliana Circadian Network Based on Non-stationary DBNs Approach with Flexible Time Lag Choosing Mechanism, in Proceedings of the IEEE International Conference on Bioinformatics & Biomedicine (BIBM'09), 2009. short paper, acceptance rate 81/233= 35%
  6. Brian Quanz, Hongliang Fei, Jun Huan, Joseph Evans, Victor Frost, Gary Minden, Daniel Deavours, Leon Searl, Daniel DePardo, Martin Kuehnhausen, Daniel Fokum, Matt Zeets, Angela Oguna, Anomaly Detection with Sensor Data for Distributed Security, in Proceedings of the International Workshop on Sensor Networks, in conjuctions with the 18th International Conference on Computer Communications and Networks (ICCCN 2009), 2009 
  7. Brian Quanz and Jun Huan, Aligned Graph Classification with Laplacian Regularized Logistic Regression, in Proceedings of the SIAM Data Mining (SDM'09), 2009
  8. Xiaohong Wang, Aaron Smalter, Jun Huan, and Gerald Lushington, G-Hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases, in Proceedings of the 12th International Conference on Extending Database Technology (EDBT'09), 2009. acceptance rate 92/283 = 32%

2008

  1. 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, in Proceedings of the IEEE International Conference on Bioinformatics and  Biomedicine (BIBM'08), 2008. acceptance rate 38/156 = 24%, PDF
  2. Seak Fei Lei, Jun Huan, Towards Site-based Function Annotations for Protein Structures. in Proceedings of the IEEE International Conference on Bioinformatics and  Biomedicine (BIBM'08), 2008. acceptance rate 38/156 = 24%, PDF,  Appendix
  3. Aaron Smalter, Jun Huan, and Gerald Lushington. A Graph Pattern Diffusion Kernel for Chemical Compound Classification. in Proceedings of the 8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE'08), 2008.
  4. Hongliang Fei, Jun Huan, Structure Feature Selection for Chemical Compound Classification, in Proceedings of the 8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE'08), 2008.
  5. Hongliang Fei, Jun Huan, Structure Feature Selection for Graph Classification, in Proceedings of the  ACM 17th Conference on Information and Knowledge Management (CIKM), 2008. acceptance rate 132/772=17%, PDF
  6. 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
  7. Aaron Smalter, Jun Huan, Gerald Lushington, Structure-based Pattern Mining For Chemical Compound Classification, in Proceedings of the 6th Asia Pacific Bioinformatics Conference (APBC), 2008. PDF

2007

  1. Xueyi Wang, Jun Huan, Jack Snoeyink,Wei Wang, Mining RNA Tertiary Motifs with Structure Graphs, in Proceedings of the 19th International Conference on Scientific and Statistical Database Management (SSDBM), 2007.
  2. 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
  3. 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

2006

  1. Jun Huan, "Graph Based Pattern Discovery in Protein Structures", Ph.D. Dissertation, Department of Computer Science, University of North Carolina, 2006
  2. 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
  3. 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 Proceedings of the IEEE Computational Systems Bioinformatics (CSB), 2006. PDF

2005

  1. Jun Huan, Deepak Bandyopadhyay, Jinze Liu, Jan Prins, Jack Snoeyink, Alexander 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

2004

  1. 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
  2. Jun Huan, Wei Wang, Deepak Bandyopadhyay, Jack Snoeyink, Jan Prins, and Alexander 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    
  3. Jun Huan, Wei Wang, Angliana Washington, Jan Prins, Ruchir Shah, and Alexander 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

2003

  1. 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
  2. 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
  3. 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 Languages and Compilers for Parallel Computing (LCPC), 2003 PDF
  4. 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

2002 & Before

  1. 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