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In Chronological Order • By Subject
Jounal Papers & Book Chapters:
- 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
- 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
- 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
- Seak Fei Lei and Jun Huan,
Towards Site-based Protein
Functional Annotations, the
International Journal of Data Mining
in Bioinformatics, 2009
- 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
- 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
- Jun Huan, Frequent
Subgraph Mining, to appear in
Encyclopedia of Database Systems, 2008
- 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.
- 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
- 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
- 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
- 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%
- 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)
- 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%
- 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%.
- 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%
- 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
- Brian Quanz and Jun Huan, Aligned Graph Classification
with Laplacian Regularized Logistic Regression, in Proceedings of the SIAM Data
Mining (SDM'09), 2009
- 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
- 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
- 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
- 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.
- 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.
- 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
- 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, in Proceedings of the 6th Asia
Pacific Bioinformatics Conference (APBC), 2008. PDF
2007
- 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.
- 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
2006
- Jun Huan, "Graph
Based Pattern Discovery in Protein Structures", Ph.D. Dissertation, Department of
Computer Science, University of North Carolina, 2006
- 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
- 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
- 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
- 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 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
- 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
- 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
- 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
- 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
- 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
- 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
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