selected publications
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academic article
- Visual Life Sciences Workflow Design Using Distributed and Heterogeneous Resources. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 17:1459-1473. 2020
- Crowd enabled curation and querying of large and noisy text mined protein interaction data. Distributed and Parallel Databases. 36:9-45. 2018
- Optimizing Phylogenetic Queries for Performance. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15:1692-1705. 2018
- Efficient and scalable labeled subgraph matching using SGMatch. Knowledge and Information Systems. 51.0:61.0-87.0. 2017
- Implementing computational biology pipelines using VisFlow. International Journal of Data Mining and Bioinformatics. 17.0:115.0-131.0. 2017
- Approximating the minimum hub cover problem on planar graphs. Optimization Letters. 10:33-45. 2016
- Improving Integration Effectiveness of ID Mapping Based Biological Record Linkage. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 12:473-486. 2015
- Top-k Similar Graph Matching Using TraM in Biological Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 9:1790-1804. 2012
- WSM: a novel algorithm for subgraph matching in large weighted graphs. Journal of Intelligent Information Systems. 38:767-784. 2012
- A natural language interface plug-in for cooperative query answering in biological databases. BMC Genomics. 13. 2012
- A Secured Collaborative Model for Data Integration in Life Sciences 2011
- An Efficient Web-Based Wrapper and Annotator for Tabular Data. International Journal of Software Engineering and Knowledge Engineering. 20:215-231. 2010
- Factors Associated with Self-Reported Depression in Arab, Chaldean, and African Americans. Ethnicity and Disease. 18:464-470. 2008
- Automatic Ontology Matching Using Application Semantics. AI Magazine. 26:21-32. 2005
- On logical foundations of multilevel secure databases. Journal of Intelligent Information Systems. 23:271-294. 2004
- Automatic composite wrapper generation for semi-structured biological data based on table structure identification. Sigmod Record. 33:58-64. 2004
- On Using Remote User Defined Functions as Wrappers for Biological Database Interoperability. International Journal of Cooperative Information Systems. 12:161-195. 2003
- Bottom-Up Association Rule Mining in Relational Databases. Journal of Intelligent Information Systems. 19:191-206. 2002
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chapter
- A Secured Collaborative Model for Data Integration in Life Sciences. Transactions On Large-scale Data- and Knowledge-centered Systems IV. 158-187. 2011
- Declarative Data Mining Using SQL3. Database Support for Data Mining Applications: Discovering Knowledge with Inductive Queries. Ed. Klemettinen, Mika. Berlin: Springer. 52-75. 2004
- Declarative Semantics Of Belief Queries In MLS Deductive Databases. Data and Application Security: Developments and Directions. 323-328. 2002
- An SQL(o) Front-End for Non-monotonic Inheritance and De-referencing. Conceptual Modeling. Springer. 52-60.
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conference paper
- Computational thinking with the web crowd using CodeMapper. 34th ACM/SIGAPP Symposium on Applied Computing. 2019
- Meet Cyrus: The Query by Voice Mobile Assistant for the Tutoring and Formative Assessment of SQL Learners. 34th ACM/SIGAPP Symposium on Applied Computing. 2019
- VisFlow: A visual database integration and workflow querying system. 33rd IEEE International Conference on Data Engineering (ICDE 2017. 2017
- Design of Declarative Graph Query Languages: On the Choice between Value, Pattern and Object Based Representations for Graphs. IEEE 28th International Conference on Data Engineering Workshops (ICDEW) 2012. 178-185. 2012
- IsoKEGG: A logic based system for querying biological pathways in KEGG. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2010. 626-631. 2011
- Toward a Cooperative Natural Language Query Interface for Biological Databases. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2011 . 556-561. 2011
- Algebraic operator support for semantic data fusion in extended SQL. IEEE 9th International Conference on Cybernetic Intelligent Systems (CIS) 2010 . 1-6. 2010
- ArrayQ: Querying Microarray Expressions for Relevant Pathways. Ninth IEEE International Conference on Bioinformatics and BioEngineering, 2009 (BIBE '09). 290-294. 2009
- A Novel Knowledge Representation Framework for Computing Sub-Graph Isomorphic Queries in Interaction Network Databases. 21st International Conference on Tools with Artificial Intelligence, 2009 (ICTAI '09). 131-138. 2009
- An Algebraic Language for Semantic Data Integration on the Hidden Web. IEEE International Conference on Semantic Computing, 2009 (ICSC '09) . 237-244. 2009
- EpICS: A system for genome-wide epistasis and genetic variation analysis using protein-protein interactions. IEEE International Conference on Bioinformatics and Biomedicine Workshop, 2009 (BIBMW 2009). 261-266. 2009
- FastWrap: An efficient wrapper for tabular data extraction from the web. IEEE International Conference on Information Reuse & Integration, 2009 (IRI '09). 354-359. 2009
- Hypothesis Driven Secondary Network Mining from PubMed Using Epiphany. International Association of Computer Science and Information Technology - Spring Conference, 2009 (IACSITSC '09). 483-487. 2009
- OWL that can Choose to Inherit and Hide it Too. IEEE International Conference on Semantic Computing, 2009 (ICSC '09). 318-323. 2009
- Online Discovery and Refinement of Novel Genes Using GeneScope. Ninth IEEE International Conference on Bioinformatics and BioEngineering, 2009 (BIBE '09). 115-122. 2009
- OntoMatch: A monotonically improving schema matching system for autonomous data integration. IEEE International Conference on Information Reuse & Integration, 2009 (IRI '09). 318-323. 2009
- Ontology guided autonomous label assignment in wrapper induced tables with missing column names. IEEE International Conference on Information Reuse & Integration, 2009 (IRI '09). 424-425. 2009
- The Power of Declarative Languages: A Comparative Exposition of Scientific Workflow Design Using BioFlow and Taverna. 2009 World Conference on Services. 322-329. 2009
- BioFlow: A Web-Based Declarative Workflow Language for Life Sciences. IEEE Congress on Services - Part I, 2008. 453-460. 2008
- PhyQL: A Web-Based Phylogenetic Visual Query Engine. IEEE International Conference on Bioinformatics and Biomedicine, 2008 (BIBM '08). 295-298. 2008
- Autonomic Wrapper Induction using Minimal Type System from Web Data. epia 2005. portuguese conference on Artificial intelligence, 2005. 130-135. 2007
- Logic-Based Association Rule Mining in XML Documents. Advanced Web and Network Technologies, and Applications (APWeb) 2006. Proceedings. 2006
- OntoBuilder: Fully Automatic Extraction and Consolidation of Ontologies from Web Sources. Proceedings of the 20th International Conference on Data Engineering. 2004
- Streamlining Biological Data Analysis Using BioFlow. 3rd IEEE International Symposium on BioInformatics and BioEngineering. 2003
- Automatic Wrapper Generation for Semi-Structured Biological Data Based on Table Structure Identification. Database and Expert Systems Applications (DEXA), 2003. Proceedings. 55-59. 2003
- A Model Theoretic Semantics for Multi-level Secure Deductive Databases. Proceedings of Logic Programming, 18th International Conference, ICLP 2002. 2002
- A Model Theoretic Semantics for Multilevel Secure Deductive Databases. Logic Programming (ICLP) 2002. Proceedings. 130-147. 2002
- An object-oriented extension of XML for autonomous web applications. Information and Knowledge Management (ACM CIKM), 2002. Proceedings. 2002
- Implementation of a Least Fixpoint Operator for Fast Mining of Relational Databases. IEEE International Conference on Data Mining (ICDM) 2002. Proceedings. 633-636. 2002
- Leveraging Dynamic Inheritance in Complex Ontology Representation. On the Move to Meaningful Internet Systems (CoopIS, DOA, and ODBASE) 2002. Proceedings. 525-525. 2002
- A view selection tool for multidimentional databases. Engineering of Intelligent Systems (IEA/AIE) 2001. Proceedings. 237-246. 2001
- Ad hoc association rule mining as SQL3 queries. IEEE International Conference on Data Mining (ICDM), 2001. Proceeedings. 609-612. 2001
- Mining first-order knowledge bases for association rules. Proceedings of the 13th International Conference on Tools with Artificial Intelligence. 218-227. 2001
- On the Equivalence of Top-down and Bottom-up Data Mining in Relational Databases. Data Warehousing and Knowledge Discovery (DaWaK) 2001. Proceedings. 41-50. 2001
- Querying phylogenies visually. Proceedings of the IEEE 2nd International Symposium on Bioinformatics and Bioengineering Conference, 2001. 3-10. 2001
- Supporting Remote User Defined Functions in Heterogeneous Biological Databases. Proceedings of the IEEE 2nd International Symposium on Bioinformatics and Bioengineering Conference, 2001. 2001
- The Use of Machine-Generated Ontologies in Dynamic Information Seeking. Cooperative Information Systems (CoopIS) 2001. Proceedings. 433-447. 2001
- Towards a Visual Query Interface for Phylogenetic Databases. Information and Knowledge Management (ACM CIKM), 2001. Proceedings. 57-64. 2001
- Achieving interoperability of genome databases through intelligent Web mediators. Bioinformatics and Biomedical Engineering (BIBE): IEEE International Symposium, 2000. Proceedings. 118-125. 2000
- GQL: a reasonable complex SQL for genomic databases. Bioinformatics and Biomedical Engineering (BIBE): IEEE International Symposium, 2000. Proceedings. 50-59. 2000