Homepage of Dr. Jason T. L. Wang: Publications

	Dr. Jason T. L. Wang Professor and Director, Data and Knowledge Engineering Lab

Dr. Jason T. L. Wang

Professor and Director, Data and Knowledge Engineering Lab

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Selected Books and Proceedings

Proceedings of the 2003 ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2003)

Proceedings of the 2002 ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2002)

Proceedings of the 2001 ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2001)

Book on Computational Intelligence and Pattern Analysis in Biological Informatics

Book on Soft Computing Analysis of Biological Data

Book on Data Mining in Bioinformatics

Book on Bioinformatics

Book on Web Data Mining

Book on Biological Pattern Discovery

Selected Publications

A partial list of publications in DBLP Bibliography Server.

A partial list of publications in PubMed.

A partial list of publications in Google Scholar.

A partial list of publications in Scirus Search Engine.

A partial list of publications in Scopus.

A partial list of publications in Collection of Computer Science Bibliographies.


Xin Zhang, Dennis Shasha, Yang Song and Jason T. L. Wang, "Fast Elastic Peak Detection for Mass Spectrometry Data Mining," IEEE Transactions on Knowledge and Data Engineering, Vol. 24, No. 4, 2012, pp. 634-648. [pdf]

Christian Laing, Dongrong Wen, Jason T. L. Wang and Tamar Schlick, "Predicting Coaxial Helical Stacking in RNA Junctions," Nucleic Acids Research, Vol. 40, No. 2, 2012, pp. 487-498. [PubMed]

Stephen J. Griesmer, Miguel Cervantes-Cervantes, Yang Song and Jason T. L. Wang, "In Silico Prediction of Noncoding RNAs Using Supervised Learning and Feature Ranking Methods," International Journal of Bioinformatics Research and Applications, Vol. 7, No. 4, 2011, pp. 355-375. [pdf] [PubMed]

Vandanaben Patel, Jason T. L. Wang, Shefali Setia, Anurag Verma, Charles D. Warden and Kaizhong Zhang, "On Comparing Two Structured RNA Multiple Alignments," Journal of Bioinformatics and Computational Biology, Vol. 8, No. 6, 2010, pp. 967-980.

Richipal Singh Bindra, Jason T. L. Wang and Paramjeet Singh Bagga, "Bioinformatics Methods for Studying MicroRNA and ARE-Mediated Regulation of Post-Transcriptional Gene Expression," International Journal of Knowledge Discovery in Bioinformatics, Vol. 1, No. 3, 2010, pp. 97-112. [pdf]

Kevin Byron, M. Cervantes-Cervantes, Jason T. L. Wang, W.C. Lin and Y. Park, "Mining roX1 RNA in Drosophila Genomes Using Covariance Models," International Journal of Computational Bioscience, Vol. 1, No. 1, 2010, pp. 22-32.

Junilda Spirollari, Jason T. L. Wang, Kaizhong Zhang, Vivian Bellofatto, Yongkyu Park and Bruce A. Shapiro, "Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization," Bioinformatics and Biology Insights, Vol. 3, June 2009, pp. 51-69.

Dongrong Wen and Jason T. L. Wang, "Design of an RNA Structural Motif Database," International Journal of Computational Intelligence in Bioinformatics and Systems Biology, Vol. 1, No. 1, 2009, pp. 32-41.

Mugdha Khaladkar, Vandanaben Patel, Vivian Bellofatto, Jeffrey Wilusz and Jason T. L. Wang, "Detecting Conserved Secondary Structures in RNA Molecules Using Constrained Structural Alignment," Computational Biology and Chemistry, Vol. 32, No. 4, August 2008, pp. 264-272. [PubMed]

Mugdha Khaladkar, Jianghui Liu, Dongrong Wen, Jason T. L. Wang and Bin Tian, "Mining Small RNA Structure Elements in Untranslated Regions of Human and Mouse mRNAs Using Structure-Based Alignment," BMC Genomics, 9:189, 2008. [PubMed]

Sen Zhang and Jason T. L. Wang, "Discovering Frequent Agreement Subtrees from Phylogenetic Data," IEEE Transactions on Knowledge and Data Engineering, Vol. 20, No. 1, January 2008, pp. 68-82. [pdf]

Mugdha Khaladkar, Vivian Bellofatto, Jason T. L. Wang, Bin Tian and Bruce A. Shapiro, "RADAR: A Web Server for RNA Data Analysis and Research," Nucleic Acids Research, Vol. 35, Web Server Issue, 2007, pp. W300-W304. [PubMed]

Katherine G. Herbert and Jason T. L. Wang, "Biological Data Cleaning: A Case Study," International Journal of Information Quality, Vol. 1, No. 1, 2007, pp. 60-82.

Jason T. L. Wang and Xiaoming Wu, "Kernel Design for RNA Classification Using Support Vector Machines," International Journal of Data Mining and Bioinformatics, Vol. 1, 2006, pp. 57-76. [PubMed]

Jason T. L. Wang, Huiyuan Shan, Dennis Shasha and William H. Piel, "Fast Structural Search in Phylogenetic Databases," Evolutionary Bioinformatics, Vol. 1, October 2005, pp. 37-46. [pdf]

Jason T. L. Wang, Xiong Wang, Dennis Shasha and Kaizhong Zhang, "MetricMap: An Embedding Technique for Processing Distance-Based Queries in Metric Spaces," IEEE Transactions on Systems, Man and Cybernetics, Part B, Cybernetics, Vol. 35, No. 5, October 2005, pp. 973-987. [pdf] [PubMed]

Jason T. L. Wang, Jianghui Liu and Junhan Wang, "XML Clustering and Retrieval through Principal Component Analysis," International Journal on Artificial Intelligence Tools, Vol. 14, No. 4, August 2005, pp. 683-699. [pdf]

Jianghui Liu, Jason T. L. Wang, Jun Hu and Bin Tian, "A Method for Aligning RNA Secondary Structures and Its Application to RNA Motif Detection," BMC Bioinformatics, 6:89, 2005, pp. 1-20. [pdf] [PubMed]

Katherine G. Herbert, Narain H. Gehani, William H. Piel, Jason T. L. Wang and Cathy H. Wu, "BIO-AJAX: An Extensible Framework for Biological Data Cleaning," ACM SIGMOD Record, Special Section on Data Engineering for Life Sciences, Vol. 33, No. 2, June 2004, pp. 51-57.

Michael M. Yin and Jason T. L. Wang, "GeneScout: A Data Mining System for Predicting Vertebrate Genes in Genomic DNA Sequences," Information Sciences, Special Issue on Soft Computing Data Mining, Vol. 163, Issues 1-3, June 2004, pp. 201-218. [pdf]

Sen Zhang, Jason T. L. Wang and Katherine G. Herbert, "XML Query by Example," International Journal of Computational Intelligence and Applications, Special Issue on Internet-Based Intelligent Systems, Vol. 2, No. 3, 2002, pp. 329-337. [html]

Xiong Wang, Jason T. L. Wang, Dennis Shasha, Bruce A. Shapiro, Isidore Rigoutsos and Kaizhong Zhang, "Finding Patterns in Three Dimensional Graphs: Algorithms and Applications to Scientific Data Mining," IEEE Transactions on Knowledge and Data Engineering, Vol. 14, No. 4, July/August 2002, pp. 731-749. [postscript] [pdf]

Jason T. L. Wang, Kaizhong Zhang, George Chang and Dennis Shasha, "Finding Approximate Patterns in Undirected Acyclic Graphs," Pattern Recognition, Vol. 35, 2002, pp. 473-483. [postscript] [pdf]

Qicheng Ma, Jason T. L. Wang, Dennis Shasha and Cathy H. Wu, "DNA Sequence Classification via an Expectation Maximization Algorithm and Neural Networks: A Case Study," IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews, Special Issue on Knowledge Management, Vol. 31, No. 4, November 2001, pp. 468-475. [postscript] [pdf]

Michael M. Yin and Jason T. L. Wang, "Effective Hidden Markov Models for Detecting Splicing Junction Sites in DNA Sequences," Information Sciences, Special Issue on Bioinformatics, Vol. 139, 2001, pp. 139-163. [pdf]

Jason T. L. Wang, Qicheng Ma, Dennis Shasha and Cathy H. Wu, "New Techniques for Extracting Features from Protein Sequences," IBM Systems Journal, Special Issue on Deep Computing for the Life Sciences, Vol. 40, No. 2, 2001, pp. 426-441. [postscript] [pdf] [html]

Jason T. L. Wang and Kaizhong Zhang, "Finding Similar Consensus between Trees: An Algorithm and a Distance Hierarchy," Pattern Recognition, Vol. 34, No. 1, January 2001, pp. 127-137 (Honorable Mention Winner of the 28th Annual Pattern Recognition Society Award).

Jason T. L. Wang and Kaizhong Zhang, "Identifying Consensus of Trees through Alignment," Information Sciences, Vol. 126, No. 1-4, 2000, pp. 165-189.

Xiong Wang, Jason T. L. Wang, King-Ip Lin, Dennis Shasha, Bruce A. Shapiro and Kaizhong Zhang, "An Index Structure for Data Mining and Clustering," Knowledge and Information Systems, Vol. 2, No. 2, May 2000, pp. 161-184. [postscript] [pdf]

Xiong Wang and Jason T. L. Wang, "Fast Similarity Search in Three-Dimensional Structure Databases," Journal of Chemical Information and Computer Sciences, Vol. 40, No. 2, 2000, pp. 442-451. [html]

Qicheng Ma and Jason T. L. Wang, "Biological Data Mining Using Bayesian Neural Networks: A Case Study," International Journal on Artificial Intelligence Tools, Special Issue on Biocomputing, Vol. 8, No. 4, 1999, pp. 433-451.

Jason T. L. Wang, Kaizhong Zhang and Chia-Yo Chang, "Identifying Approximately Common Substructures in Trees Based on a Restricted Edit Distance," Information Sciences, Vol. 121, No. 3-4, 1999, pp. 367-386.

Marcus J. Healey, Jason T. L. Wang, George Chang, Amit Revankar and Gunjan Samtani, "Precise Environmental Searches: EnviroDaemon with Hierarchical Information Search," Environmental Quality Management, Vol. 9, No. 1, 1999, pp. 51-62.

Jason T. L. Wang, Steve Rozen, Bruce A. Shapiro, Dennis Shasha, Zhiyuan Wang and Maisheng Yin, "New Techniques for DNA Sequence Classification," Journal of Computational Biology, Vol. 6, No. 2, 1999, pp. 209-218. [postscript] [pdf] [PubMed]

Jason T. L. Wang, Bruce A. Shapiro, Dennis Shasha, Kaizhong Zhang and Kathleen M. Currey, "An Algorithm for Finding the Largest Approximately Common Substructures of Two Trees," IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 20, No. 8, August 1998, pp. 889-895. [postscript] [pdf]

Chia-Yo Chang, Jason T. L. Wang and Roger K. Chang, "Scientific Data Mining: A Case Study," International Journal of Software Engineering and Knowledge Engineering, Vol. 8, No. 1, 1998, pp. 77-96.

C.-S. Wei, Q. Liu, Jason T. L. Wang and Peter A. Ng, "Knowledge Discovering for Document Classification Using Tree Matching in TEXPROS," Information Sciences, Vol. 100, Nos. 1-4, August 1997, pp. 255-310.

Jason T. L. Wang and Chia-Yo Chang, "Fast Retrieval of Electronic Messages That Contain Mistyped Words or Spelling Errors," IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics, Vol. 27, No. 3, June 1997, pp. 441-451. [pdf]

Gang Zhou, Jason T. L. Wang and Peter A. Ng, "Curriculum Knowledge Representation and Manipulation in Knowledge-Based Tutoring Systems," IEEE Transactions on Knowledge and Data Engineering, Vol. 8, No. 5, October 1996, pp. 679-689. [pdf]

Xiaolong Hao, Jason T. L. Wang and Peter A. Ng, "Information Extraction from the Structured Part of Office Documents," Information Sciences, Vol. 91, Nos. 3&4, June 1996, pp. 245-274.

Jason T. L. Wang, Thomas G. Marr, Dennis Shasha, Bruce A. Shapiro, Gung-Wei Chirn and T. Y. Lee, "Complementary Classification Approaches for Protein Sequences," Protein Engineering, Vol. 9, No. 5, May 1996, pp. 381-386. [PubMed]

Kaizhong Zhang, Jason T. L. Wang and Dennis Shasha, "On the Editing Distance between Undirected Acyclic Graphs," International Journal of Foundations of Computer Science, Special Issue on Computational Biology, Vol. 7, No. 1, March 1996, pp. 43-57. [postscript] [pdf]

Fortune Mhlanga, Zhijian Zhu, Jason T. L. Wang and Peter A. Ng, "A New Approach to Modeling Personal Office Documents," Data and Knowledge Engineering, Vol. 17, 1995, pp. 127-158.

Jason T. L. Wang, Kaizhong Zhang and Gung-Wei Chirn, "Algorithms for Approximate Graph Matching," Information Sciences, Vol. 82, 1995, pp. 45-74.

Zhijian Zhu, James McHugh, Jason T. L. Wang and Peter A. Ng, "A Formal Approach to Modeling Office Information Systems," Journal of Systems Integration, Vol. 4, No. 4, December 1994, pp. 373-403.

Jason T. L. Wang, Thomas G. Marr, Dennis Shasha, Bruce A. Shapiro and Gung-Wei Chirn, "Discovering Active Motifs in Sets of Related Protein Sequences and Using Them for Classification," Nucleic Acids Research, Vol. 22, No. 14, Aug. 1994, pp. 2769-2775. [postscript] [pdf] [PubMed]

Jason T. L. Wang, Kaizhong Zhang, Karpjoo Jeong and Dennis Shasha, "A System for Approximate Tree Matching," IEEE Transactions on Knowledge and Data Engineering, Vol. 6, No. 4, August 1994, pp. 559-571. [postscript] [pdf]

Xiaolong Hao, Jason T. L. Wang, Michael Bieber and Peter A. Ng, "Heuristic Classification of Office Documents," International Journal on Artificial Intelligence Tools, Vol. 3, No. 2, 1994, pp. 233-265.

Dennis Shasha, Jason T. L. Wang, Kaizhong Zhang and Frank Y. Shih, "Exact and Approximate Algorithms for Unordered Tree Matching," IEEE Transactions on Systems, Man and Cybernetics, Vol. 24, No. 4, April 1994, pp. 668-678. [pdf]

Kaizhong Zhang, Dennis Shasha and Jason T. L. Wang, "Approximate Tree Matching in the Presence of Variable Length Don't Cares," Journal of Algorithms, Vol. 16, No. 1, January 1994, pp. 33-66. [postscript] [pdf]

Q. Liu, Jason T. L. Wang and Peter A. Ng, "On Research Issues Regarding Uncertain Query Processing in an Office Document Retrieval System," Journal of Systems Integration, Vol. 3, No. 2, June 1993, pp. 163-194.

Jason T. L. Wang and Peter A. Ng, "TEXPROS: An Intelligent Document Processing System," International Journal of Software Engineering and Knowledge Engineering, Vol. 2, No. 2, June 1992, pp. 171-196.

Dennis Shasha and Tsong-Li Wang, "Optimizing Equi-Join Queries in Distributed Databases where Relations are Hash Partitioned," ACM Transactions on Database Systems, Vol. 16, No. 2, June 1991, pp. 279-308. [pdf]

Dennis Shasha and Tsong-Li Wang, "New Techniques for Best-Match Retrieval," ACM Transactions on Information Systems, Vol. 8, No. 2, April 1990, pp. 140-158; also appeared in ACM Computing Reviews, Vol. 32, June 1991, pp. 9106-0454. [pdf]


Katherine G. Herbert, Junilda Spirollari, Jason T. L. Wang, William H. Piel, John Westbrook, Winona C. Barker, Zhang-Zhi Hu and Cathy H. Wu, "Bioinformatic Databases," in Wiley Encyclopedia of Computer Science and Engineering, (ed. Benjamin Wah), John Wiley & Sons, Inc., 2008, pp. 561:1-561:10.

Jason T. L. Wang, Dongrong Wen, Bruce A. Shapiro, Katherine G. Herbert, Jing Li and Kaushik Ghosh, "Toward an Integrated RNA Motif Database," Proceedings of the 4th International Workshop on Data Integration in the Life Sciences (DILS 2007), Philadelphia, Pennsylvania, June 2007, pp. 27-36.

Mugdha Khaladkar and Jason T. L. Wang, "Detecting Conserved RNA Secondary Structures in Viral Genomes: The RADAR Approach," Proceedings of the 2007 NSF Workshop on Biosurveillance Systems and Case Studies (Biosurveillance 2007), New Brunswick, New Jersey, May 2007, pp. 222-227. [pdf]

Sen Zhang, Katherine G. Herbert, Jason T. L. Wang, William H. Piel and David R. B. Stockwell, "PhyloMiner: A Tool for Evolutionary Data Analysis," Proceedings of the 18th International Conference on Scientific and Statistical Database Management (SSDBM 2006), Vienna, Austria, July 2006, pp. 129-132.

Sen Zhang and Jason T. L. Wang, "Mining Frequent Agreement Subtrees in Phylogenetic Databases," Proceedings of the 6th SIAM International Conference on Data Mining (SDM 2006), Bethesda, Maryland, April 2006, pp. 222-233.

Katherine G. Herbert, Shashikanth Pusapati, Jason T. L. Wang and William H. Piel, "Lineage Path Integration for Phylogenetic Resources," Proceedings of the 17th International Conference on Scientific and Statistical Database Management (SSDBM 2005), Santa Barbara, California, June 2005, pp. 117-120. [pdf]

David R. B. Stockwell and Jason T. L. Wang, "Biomonitoring, Phylogenetics and Anomaly Aggregation Systems," Proceedings of the 3rd IEEE International Conference on Intelligence and Security Informatics (ISI 2005), Atlanta, Georgia, May 2005, pp. 523-529.

Katherine G. Herbert, Jason T. L. Wang and Jianghui Liu, "Information Retrieval and Data Mining," in Computer Science Handbook, 2nd edition, (ed. A. B. Tucker), Chapter 75, CRC Press, 2004, pp. 75.1-75.16.

Dennis Shasha, Jason T. L. Wang and Sen Zhang, "Unordered Tree Mining with Applications to Phylogeny," Proceedings of the 20th International Conference on Data Engineering (ICDE 2004), Boston, Massachusetts, April 2004, pp. 708-719. [pdf]

Jason T. L. Wang, Huiyuan Shan, Dennis Shasha and William H. Piel, "TreeRank: A Similarity Measure for Nearest Neighbor Searching in Phylogenetic Databases," Proceedings of the 15th International Conference on Scientific and Statistical Database Management (SSDBM 2003), Cambridge, Massachusetts, July 2003, pp. 171-180. [pdf]

Michael M. Yin and Jason T. L. Wang, "Mining Genes in DNA Using GeneScout," Proceedings of the 2002 IEEE International Conference on Data Mining (ICDM 2002), Maebashi City, Japan, December 2002, pp. 733-736. [postscript] [pdf]

Huiyuan Shan, Katherine G. Herbert, William H. Piel, Dennis Shasha and Jason T. L. Wang, "A Structure-Based Search Engine for Phylogenetic Databases," Proceedings of the 14th International Conference on Scientific and Statistical Database Management (SSDBM 2002), Edinburgh, Scotland, July 2002, pp. 7-10. [postscript] [pdf]

Dennis Shasha, Jason T. L. Wang, Huiyuan Shan and Kaizhong Zhang, "ATreeGrep: Approximate Searching in Unordered Trees," Proceedings of the 14th International Conference on Scientific and Statistical Database Management (SSDBM 2002), Edinburgh, Scotland, July 2002, pp. 89-98. [postscript] [pdf]

Dennis Shasha, Jason T. L. Wang and Rosalba Giugno, "Algorithmics and Applications of Tree and Graph Searching," Proceedings of the 21st ACM SIGMOD-SIGACT-SIGART Symposium on Principles of Database Systems (PODS 2002), Madison, Wisconsin, June 2002, pp. 39-52. [postscript] [pdf] [talk slides in powerpoint]

Qicheng Ma, Jason T. L. Wang and James R. Gattiker, "Mining Biomolecular Data Using Background Knowledge and Artificial Neural Networks," in Handbook of Massive Data Sets, (eds. J. Abello, P. M. Pardalos and M. G. C. Resende), Chapter 30, Kluwer Academic Publishers, 2002, pp. 1141-1168. [postscript] [pdf]

Jason T. L. Wang, Qicheng Ma and Katherine G. Herbert, "Software Engineering and Knowledge Engineering Issues in Bioinformatics," in Handbook of Software Engineering and Knowledge Engineering, Vol. 1, Fundamentals, (ed. S. K. Chang), Chapter 30, World Scientific Publishing Company, 2001, pp. 719-732. [postscript] [pdf]

Jason T. L. Wang, Qicheng Ma, Dennis Shasha and Cathy H. Wu, "Application of Neural Networks to Biological Data Mining: A Case Study in Protein Sequence Classification," Proceedings of the 6th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2000), Boston, Massachusetts, August 2000, pp. 305-309. [postscript] [pdf]

Jason T. L. Wang, Xiong Wang, Dennis Shasha, Bruce A. Shapiro, Kaizhong Zhang, Qicheng Ma and Zasha Weinberg, "An Approximate Search Engine for Structural Databases," Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD 2000), Dallas, Texas, May 2000, pp. 584. [postscript] [pdf]

Jason T. L. Wang, Xiong Wang, King-Ip Lin, Dennis Shasha, Bruce A. Shapiro and Kaizhong Zhang, "Evaluating a Class of Distance-Mapping Algorithms for Data Mining and Clustering," Proceedings of the 5th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 1999), San Diego, California, August 1999, pp. 307-311.

Xiong Wang, Jason T. L. Wang, Dennis Shasha, Bruce A. Shapiro, Sitaram Dikshitulu, Isidore Rigoutsos and Kaizhong Zhang, "Automated Discovery of Active Motifs in Three Dimensional Molecules," Proceedings of the 3rd International Conference on Knowledge Discovery and Data Mining (KDD 1997), Newport Beach, California, August 1997, pp. 89-95. [postscript] [pdf]

Jason T. L. Wang, Dennis Shasha, George J. S. Chang, Liam Relihan, Kaizhong Zhang and Girish Patel, "Structural Matching and Discovery in Document Databases," Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD 1997), Tucson, Arizona, May 1997, pp. 560-563. [postscript]

Jason T. L. Wang, Bruce A. Shapiro, Dennis Shasha, Kaizhong Zhang and Chia-Yo Chang, "Automated Discovery of Active Motifs in Multiple RNA Secondary Structures," Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining (KDD 1996), Portland, Oregon, August 1996, pp. 70-75.

Jason T. L. Wang, Kaizhong Zhang and Dennis Shasha, "Pattern Matching and Pattern Discovery in Scientific, Program and Document Databases," Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD 1995), San Jose, CA, May 1995, pp. 487.

Jason T. L. Wang, Gung-Wei Chirn, Thomas G. Marr, Bruce A. Shapiro, Dennis Shasha and Kaizhong Zhang, "Combinatorial Pattern Discovery for Scientific Data: Some Preliminary Results," ACM SIGMOD Record, Vol. 23, No. 2, June 1994, pp. 115-125; also appeared in Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD 1994), Minneapolis, Minnesota, May 1994.

Tsong-Li Wang and Dennis Shasha, "Query Processing for Distance Metrics," Proceedings of the 16th International Conference on Very Large Data Bases (VLDB 1990), Brisbane, Australia, Aug. 1990, pp. 602-613.