Refereed Journal Publications

1. Xin Mou and Hasan Jamil. “Visual Life Sciences Workflow Design using Distributed Heterogeneous Resources.” ACM/IEEE Transaction on Computational Biology and Bioinformatics (TCBB). IEEE Press. 2018. In press.
2. Hasan Jamil and Fereidoon Sadri. “Crowd Enabled Curation and Querying of Large and Noisy Text Mined Protein Interaction Data.” Distributed and Parallel Databases (DAPD). Volume 36, Number 1. Pages 9-45. Springer. 2018.
3. Hasan Jamil. “Optimizing Phylogenetic Queries for Performance.” ACM/IEEE Transaction on Computational Biology and Bioinformatics (TCBB). IEEE Press. 2018. Volume 15, Number 5. Pages 1692-1705.
4. Xin Mou, Hasan Jamil and Robert Rinker. “Implementing Computational Biology Pipelines using VisFlow.” International Journal of Data Mining and Bioinformatics. Volume 17, Number 2. Pages 115-131. 2017. InderScience.
5. Carlos Rivero and Hasan Jamil. “Efficient and scalable labeled subgraph matching using SGMatch.” Knowledge and Information Systems. Springer. Volume 51, Number 1. Pages 61-87. 2017.
6. Hasan Jamil. “A Visual Interface for Querying Heterogeneous Phylogenetic Databases.” ACM/IEEE Transaction on Computational Biology and Bioinformatics (TCBB). IEEE Press. Volume 14, Number 1. Pages 131-144. 2017.
7. Belma Yelbay, Ilker Birbil, Kerem Bulbul and Hasan Jamil. “Approximating the Minimum Hub Cover Problem on Planer Graphs.” Optimization Letters. Springer. March, Volume 10, Number 1. Pages 33-45. 2016.
8. Hasan Jamil. “Improving Integration Effectiveness through ID Mapping based Record Linkage in Biological Databases.” ACM/IEEE Transaction on Computational Biology and Bioinformatics (TCBB). Volume 12, Number 2. March/April, 2015. Pages 473-486. IEEE Press.
9. Kazi Zakia Sultana, Anupam Bhattacharjee and Hasan Jamil. “Querying KEGG Pathways in Logic.” International Journal of Data Mining and Bioinformatics (IJDMB). Volume 9, Number 1. 2014. Pages 1-21. InderScience Publisher.
10. Hasan Jamil. “Designing Integrated Computational Biology Pipelines Visually.” ACM/IEEE Transaction on Computational Biology and Bioinformatics (TCBB). Volume 10, Number 3. May/June, 2013. Pages 605-618. IEEE Press.
11. Hasan Jamil. “A Natural Language Interface plug-in for Cooperative Query Answering in Biological Databases.” BMC Genomics, June 11, 2012. 13(Suppl 3):S4. BioMed Central. doi:10.1186/1471-2164-13-S3-S4. Springer.
12. Shafkat Amin, Russell L. Finley, Jr. and Hasan Jamil. “Top-K Similar Graph Matching using TraM in Biological Networks.” ACM/IEEE Transaction on Computational Biology and Bioinformatics (TCBB). Volume 9, Number 6, 2012. Pages 1790-1804. IEEE Press.
13. Anupam Bhattacharjee and Hasan Jamil. “WSM: A Novel Algorithm for Subgraph Matching in Large Weighted Graphs.” Journal of Intelligent Information Systems (JIIS). Volume 38, Number 3. 2012. Pages 767-784. Springer-Verlag.
14. Anupam Bhattacharjee and Hasan Jamil. “A Schema Matching System for Autonomous Data Integration.” International Journal of Information and Decision Sciences (IJIDS). Volume 4, Issue 2/3. 2012. Pages 167-181. IEEE IRI 2009 Special Issue. InderScience Publisher.
15. Hasan Jamil.“A Secured Collaborative Model for Data Integration in Life Sciences.” Transactions on Large-Scale Data- and Knowledge Centered Systems: Database Systems for Biomedical Applications (TLDKS). Volume 4. LNCS 6990, pp. 158–187, 2011. Springer-Verlag.
16. Hasan Jamil. “Integrating Large and Distributed Life Sciences Resources for Systems Biology Research: Progress and New Challenges.” Transactions on Large-Scale Data- and Knowledge-Centered Systems (TLDKS). Volume 3. LNCS 6790, pp. 208–237, 2011. Springer-Verlag.
17. Alan Dombkowski, Kazi Zakia Sultana, Douglas Craig and Hasan Jamil. “In Silico Analysis of Combinatorial microRNA Activity Reveals Target Genes and Pathways Associated with Breast Cancer Metastasis.” Journal Cancer Informatics (CI). 2011:10 13-29. Libertas Academica Publisher. 5,195 total downloads.
18. Hasan Jamil and Aminul Islam. “Managing and Querying Gene Expression Data using Curray.” Journal BMC Proceedings. BioMed Central. 2011, 5(Suppl 2):S10. Springer.
19. Jesmin, SM Mahbubur Rashid, Hasan Jamil, Raquel Hontecillas and Josep Bassaganya-Riera. “Gene Regulatory Network Reveals Oxidative Stress as the Underlying Molecular Mechanism of Type 2 Diabetes and Hypertension.” BMC Medical Genomics. BioMed Central. 2010, 3:45. Springer.
20. Mohammad Shafkat Amin and Hasan Jamil. “An Efficient Web-based Wrapper and Annotator for Tabular Data.” International Journal of Software Engineering and Knowledge Engineering (IJSEKE). Volume 20, Issue 2. 2010. Pages 215-231. World Scientific.
21. Hasan Jamil, Aminul Islam and Shahriyar Hossain. “A Declarative Language and Toolkit for Scientific Workflow Implementation and Execution.” International Journal of Business Process Integration and Management (IJBPIM). Volume 5, Issue 1. 2010. Pages 3-17. IEEE SWF 2009 Special Issue. InderScience Publisher.
22. Ruhul Amin, Jesmin, Hasan Jamil and M. Anwar Hossain. “In silico Analysis of Human Telomerase Reverse Transcriptase (hTERT ) Gene: Identification of a Distant Homolog of Melanoma Antigen Family Gene (MAGE).” Journal Cancer Informatics (CI). 2009; 7: 171–181. Libertas Academica Publisher. 2,955 total downloads.
23. Liangyou Chen, Hasan Jamil and Nan Wang. “Automatic Composite Wrapper Generation for Semi-Structured Biological Data Based on Table Structure Identification.” ACM SIGMOD Record, Special Issue on Biological Data Management. Amarnath Gupta, Editor. Volume 33, Number 2, 2004. Pages 58-64. ACM Press.
24. Hasan Jamil and Gillian Dobbie. “On the Logical Foundations of Multi Level Secure Databases.” Journal of Intelligent Information Systems (JIIS); Special Issue on Data and Applications Security. Bhavani Thuraisingham, Editor. Volume 23, number 3, 2004. Pages 271-294. Springer-Verlag.
25. Liangyou Chen and Hasan Jamil. “On Using Remote User Defined Functions as Wrappers for Biological Database Interoperability.” International Journal of Cooperative Information Systems (IJCIS); Special Issue on Data Management and Modeling Support in Bioinformatics. Volume 12, Number 2, June 2003; Pages 161-195. World Scientific.
26. Hasan Jamil. “Bottom-up Association Rule Mining in Relational Databases.” Journal of Intelligent Information Systems (JIIS); Special Issue on Data Mining; Volume 19, Number 2, September 2002; Pages 191-206. Springer-Verlag.
27. Hasan Jamil. “Belief Reasoning in MLS Deductive Databases.” ACM SIGMOD Record; Volume 28, Number 2, June 1999. Pages 109-120. ACM Press.

Invited Journal Publications

1. Avigdor Gal, Giovanni Modica, Hasan Jamil and Ami Eyal. “Automatic Ontology Matching using Application Semantics.” Artificial Intelligence Magazine, volume 26, number 1, 2005. Pages 21-32. AAAI Press.

Non-Refereed Journal Publications

1. Hasan Jamil. “Computational Thinking in Patch.” Computing Research Repository (CoRR). June, 2017. arXiv:abs/1706.03272 [cs.PL].
2. Hasan Jamil. “Smart Assessment of and Tutoring for Computational Thinking MOOC Assignments using MindReader.” Computing Research Repository (CoRR). April, 2017. arXiv:abs/1705.00959 [cs.PL].
3. Hasan Jamil. “Knowledge Rich Natural Language Queries over Structured Biological Databases.” Computing Research Repository (CoRR). April, 2017. arXiv:abs/1703.10692 [cs.DB].
4. Carlos Rivero and Hasan Jamil. “A Novel Model for Distributed Big Data Service Composition using Stratified Functional Graph Matching.” Computing Research Repository (CoRR). July, 2016. arXiv:abs/1607.02669 [cs.DB].
5. Hasan Jamil and Fereidoon Sadri. “Reliable Querying of Very Large, Fast Moving and Noisy Predicted Interaction Data using Hierarchical Crowd Curation.” Computing Research Repository (CoRR). June, 2016. arXiv:abs/1606.01957 [cs.DB].
6. Belma Yelbay, Ilker Birbil, Kerem Bulbul and Hasan Jamil. “Trade-offs Computing Minimum Hub Cover toward Optimized Graph Query Processing.” Computing Research Repository (CoRR). November, 2013. arXiv:abs/1311.1626 [cs.DB].
7. Carlos Rivero and Hasan Jamil. “Anatomy of Graph Matching based on an XQuery and RDF Implementation.” Computing Research Repository (CoRR). November, 2013. arXiv:abs/1311.2342 [cs.DB].
8. Hasan Jamil. “Empowering Evolving Social Network Users with Privacy Rights.” Computing Research Repository (CoRR). December, 2013. arXiv:abs/1312.0189 [cs.DB].

Fully Reviewed Book Chapters

1. Hasan Jamil. “Declarative Data Mining using SQL3.” Database Technology for Data Mining, Rosa Meo and Pier Luca Lanzi, Editors. 2004. LNCS 2682. Pages 52-75. Springer-Verlag.
2. Hasan Jamil. “Declarative Semantics of Belief Queries in MLS Deductive Databases.” Data and Applications Security: Developments and Directions, Thuraisingham, van de Riet, Dittrich and Tari, Editors. 2001. Kluwer Academic Publishers.

Fully Refereed Conference Publications

1. Patrick Vanvorce and Hasan Jamil. “Computational Thinking with the Web Crowd using CodeMapper.” In the proceedings of the 34^th ACM Symposium on Applied Computing (SAC). Limassol, Cyprus. April 8-12, 2019. In Press.
2. Josue Espinosa Godinez and Hasan Jamil. “Meet Cyrus – The Query by Voice Mobile Assistant for Tutoring and Formative Assessment of SQL Learners.” In the proceedings of the 34^th ACM Symposium on Applied Computing (SAC). Limassol, Cyprus. April 8-12, 2019. In Press
3. Hasan Jamil, Xin Mou, Robert Heckendorn, Clinton Jeffery, Frederick Sheldon, Cassidy Hall and Nina Peterson. “Authoring Adaptive Digital Computational Thinking Lessons using vTutor for Web-Based Learning.” In the proceedings of the 9^th International Conference on Web-based Learning, Chiang Mai, Thailand. August 22-26, 2018. Springer LNCS series. Pages 125-131.
4. Mohammad Ashrafuzzaman, Hasan Jamil, Yacine Chakhchoukh, Frederick T. Sheldon. “A Best-Effort Damage Mitigation Model for Cyber-Attacks on Smart Grids.” IEEE 42^nd Annual Computer Software and Applications Conference, COMPSAC 2018, Tokyo, Japan, 23-27 July 2018, Volume 2. Pages 510-515.
5. Hasan Jamil. “A Free-Choice Social Learning Network for Computational Thinking.” In the proceedings of the 18^th IEEE International Conference on Advanced Learning Technologies, Mumbai, India. July 8-14, 2018. IEEE Press. Pages 69-71.
6. Robert Breckenridge and Hasan Jamil. “GreenShip: A Social Networking System for Combating Cyber-Bullying and Defending Personal Reputation.” In the proceedings of the 33^rd ACM Symposium on Applied Computing (SAC). Pau, France. DOI: 10.1145/3167132.3167326. April 9-13, 2018. ACM Press. Pages 1813-1820.
7. Hasan Jamil. “Visual Computational Thinking using Patch.” In the proceedings of the 8^th International Conference on Web-based Learning, Cape Town, South Africa. Pages 208-214. September 20-22, 2017. Springer LNCS series.
8. Hasan Jamil. “Knowledge Rich Natural Language Queries over Structured Biological Databases.” In the proceedings of the 8^th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Boston, MA, USA. Pages 352-361. August 20-23, 2017. ACM Press.
9. Hasan Jamil. “Automated Personalized Assessment of Computational Thinking MOOC Assignments.” In the proceedings of the 17^th IEEE International Conference on Advanced Learning Technologies, Timisoara, Romania. Pages 261-263. July 3-7, 2017. IEEE Press.
10. Hasan Jamil. “Efficient Top-k Shortest Path Query Processing in Sparse Graph Databases.” In the proceedings of the 7^th ACM International Conference on Web Intelligence, Mining and Semantics, Amantea, Italy. Pages 9:1-9:10. June 19-22, 2017. ACM Press.
11. Hasan Jamil and Carlos Rivero. “A Novel Model for Distributed Big Data Service Composition using Stratified Functional Graph Matching.” In the proceedings of the 7^th ACM International Conference on Web Intelligence, Mining and Semantics, Amantea, Italy. 34:1-34:8. June 19-22, 2017. ACM Press.
12. Xin Mou, Hasan Jamil and Marshall Ma. “VisFlow: A Visual Database Integration and Workflow Querying System.” In the proceedings of the IEEE International Conference on Data Engineering, San Diego, CA, USA. Pages 1421-1422. April 19-22, 2017. IEEE Press.
13. Hasan Jamil. “Using Stratified Privacy for Personal Reputation Defense in Online Social Networks.” In the proceedings of the 32^nd ACM Symposium on Applied Computing (SAC). Marrakech, Morocco. Pages 1037-1044. April 3-7, 2017. ACM Press.
14. Xin Mou, Hasan Jamil and Robert Rinker. “Visual Orchestration and Autonomous Execution of Distributed and Heterogeneous Computational Biology Pipelines.” In the proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, China. Pages 752-757 December 15-19, 2016. IEEE Press.
15. Hasan Jamil. “Pruning Forests to Find the Trees.” In the proceedings of the 28^th ACM International Conference on Scientific and Statistical Database Management (SSDBM), Budapest, Hungary, July 18-20, 2016. Pages 18:1-18:12. ACM Press.
16. Hasan Jamil and Fereidoon Sadri. “Hierarchical Crowd Curation of Very Large and Predicted Protein-Protein Interaction Data.” In the proceedings of the 20^th International Database Engineering & Applications Symposium (IDEAS), Montreal, Canada, July 11-13, 2016. Pages 316-321. ACM Press.
17. Hasan Jamil. “MapBase: Declaratively Approaching Quality ID Mapping using an On-Demand Data Warehouse.” In the proceedings of the 8^th International Conference on Bioinformatics and Computational Biology (BICoB), Las Vegas, April 4-6, 2016. Pages 83-88.
18. Hasan Jamil and H. V. Jagadish. “A Structured Query Model for the Deep Relational Web.” ACM International Conference on Information and Knowledge Management (CIKM), Melbourne, Australia. October 2015. Pages 1679-1682. ACM Press.
19. Carlos Rivero and Hasan Jamil. “A Novel Model for Distributed Big Data Service Composition using Functional Graph Matching.” IEEE International Congress on Big Data (BigData). Anchorage, Alaska. Pages 794-795. June 2014. IEEE Press.
20. Anupam Bhattacharjee and Hasan Jamil. “CodeBlast: A Two-Stage Algorithm for Improved Program Similarity Matching in Large Software Repositories.” ACM Symposium on Applied Computing (SAC). Coimbra, Portugal, March 18-23, 2013. Pages 846-852. ACM Press.
21. Hasan Jamil. “Toward a Cooperative Natural Language Query Interface for Biological Databases.” IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Atlanta, Georgia, November 12-15, 2011. Pages 556-561. IEEE Press.
22. Akther Shermin, Hasan Jamil and Mehmet A. Orgun. “A Scalable Approach for Inferring Transcriptional Regulation in the Yeast Cell Cycle.” ACM Conference on Bioinformatics, Computational Biology and Biomedicine (BCB). Chicago, Illinois, August 1-3, 2011. Pages 345-349. ACM Press.
23. Hasan Jamil. “Computing Subgraph Isomorphic Queries using Structural Unification and Minimum Graph Structures.” ACM International Symposium on Applied Computing (SAC), Taichung, Taiwan. March 2011. Pages 1053-1058. ACM Press.
24. Kazi Zakia Sultana, Anupam Bhattacharjee and Hasan Jamil. “IsoKEGG: A Logic based System for Querying Biological Pathways in KEGG.” IEEE International Conference on Bioinformatics & BioMedicine (BIBM). Hong Kong. December 2010. Pages 626-631. IEEE Press.
25. Saikat Dey and Hasan Jamil. “A Hierarchical Approach to Reachability Query Answering in Very Large Graph Databases.” ACM International Conference on Information and Knowledge Management (CIKM), Toronto, Canada. November 2010. Pages 1377-1380. ACM Press.
26. Hasan Jamil. “Talking Biology in Logic, and Back.” In the Proceedings of the International Conference on Knowledge-based and Intelligent Information & Engineering Systems (KES). Cardiff, Wales, UK. LNAI 6278. September, 2010. Pages 408-417. Springer-Verlag.
27. Shahriyar Hossain and Hasan Jamil. “A Hybrid Index Structure for Set-valued Attributes using Itemset Tree and Inverted List.” International Conference on Database Expert System Applications (DEXA), Bilbao, Spain. LNCS 6261. August 2010. Pages 349-357. Springer-Verlag.
28. Mohammad Shafkat Amin, Anupam Bhattacharjee and Hasan Jamil. “Wikipedia Driven Autonomous Label Assignment in Wrapper Induced Tables with Missing Column Names.” ACM International Symposium on Applied Computing (SAC), Sierre, Switzerland, March 2010. Pages 1656-1660. ACM Press.
29. Mohammad Shafkat Amin, Anupam Bhattacharjee and Hasan Jamil. “A Cytoscape based Integrative Framework for Efficient Sub-graph Isomorphic Protein-Protein Interaction Motif Lookup.” ACM International Symposium on Applied Computing (SAC), Sierre, Switzerland, March 2010. Pages 1572-1576. ACM Press.
30. Mohammad Shafkat Amin, Anupam Bhattacharjee, Russell L. Finley and Hasan Jamil. “A Stochastic Approach to Candidate Disease Gene Subnetwork Extraction.” ACM International Symposium on Applied Computing (SAC), Sierre, Switzerland, March 2010. Pages 1534-1538. ACM Press.
31. Hasan Jamil. “A Novel Knowledge Representation Framework for Computing Sub-Graph Isomorphic Queries in Interaction Network Databases.” In the Proceedings of the 21st IEEE International Conference on Tools with Artificial Intelligence (ICTAI), Newark, New Jersey. November 2009. Pages 131-138. IEEE Press.
32. Shazzad Hosain and Hasan Jamil. “Algebraic Operator Support for Semantic Data Fusion in Extended SQL.” In the Proceedings of the 8th IEEE International Conference on Cybernetic Intelligent Systems (CIS). Birmingham, UK. 2009. Pages 220-225. IEEE Press.
33. Hasan Jamil. “An Efficient Logic Programming Approach to Sub-Graph Isomorphic Queries.” In the Proceedings of the International Conference on Applications of Declarative Programming and Knowledge Management (INAP); Evora, Portugal. Springer. November 2009. Pages 83-96.
34. Saied Haidarian Shahri and Hasan Jamil. “An Extendable Meta-Learning Algorithm for Ontology Mapping.” In the Proceedings of the 8th International Conference on Flexible Query Answering Systems (FQAS); Denmark. LNAI 5822. October 2009. Pages 418-430. Springer-Verlag.
35. Kazi Zakia Sultana, Anupam Bhattacharjee, Mohammad Shafkat Amin and Hasan Jamil. “A Model for Contextual Cooperative Query Answering in E-Commerce Applications.” In the Proceedings of the 8th International Conference on Flexible Query Answering Systems (FQAS); Roskilde, Denmark. LNAI 5822. October 2009. Pages 25-36. Springer-Verlag.
36. Shafkat Amin and Hasan Jamil. “FastWrap: Efficient Wrapper Generation for Tabular Web Data Extraction.” IEEE International Conference on Information Reuse and Integration (IRI), Nevada. August 2009. Pages 354-359. IEEE Press.
37. Mohammad Shafkat Amin and Hasan Jamil. “Ontology Guided Autonomous Label Assignment in Wrapper Induced Tables with Missing Column Names.” In the Proceedings of the IEEE International Conference on Information Reuse and Integration (IRI); Las Vegas, Nevada, United States. August 2009. Pages 424-425. IEEE Press.
38. Anupam Bhattacharjee, Aminul Islam, Hasan Jamil and Derek Wildman. “IDChase: Mitigating Identifier Migration Trap in Biological Databases.” The Second International Conference on Contemporary Computing (IC3), Noida, India, 2009. Springer CCIS 40. Pages 461-472. Springer-Verlag.
39. Shazzad Hosain and Hasan Jamil. “An Algebraic Foundation for Semantic Data Integration on the Hidden Web.” IEEE International Conference on Semantic Computing (ICSC), California, 2009. Pages 237-244. IEEE Press.
40. Shazzad Hosain and Hasan Jamil. “OWL that can Choose to Inherit and Hide it Too.” IEEE International Conference on Semantic Computing (ICSC), California, 2009. Pages 318-323. IEEE Press.
41. Anupam Bhattacharjee, Aminul Islam, Mohammad Shafkat Amin, Shahriyar Hossain, Shazzad Hosain, Hasan Jamil and Leonard Lipovich. “On-the-fly Integration and ad hoc Querying of Life Sciences Databases using LifeDB.” International Conference on Database Expert System Applications (DEXA), Austria, 2009. LNCS 5690. Pages 561-575. Springer-Verlag.
42. Anupam Bhattacharjee and Hasan Jamil “OntoMatch: A Monotonically Improving Schema Matching System for Autonomous Data Integration.” IEEE International Conference on Information Reuse and Integration (IRI), Nevada. August 2009. Pages 318-323. IEEE Press.
43. Hasan Jamil and Jesmin. “Online Discovery and Refinement of Novel Genes using GeneScope.” IEEE International Conference on Bioinformatics and Bioengineering (BIBE), Taiwan, June 2009. Pages 115-122. IEEE Press.
44. Shahriyar Hossain, Cherie M. Southwood, Hasan Jamil and Alexander Gow. “Using ArrayQ for Mapping Gene Expressions to Pathways.” IEEE International Conference on Bioinformatics and Bioengineering (BIBE), Taiwan, June 2009. Pages 290-294. IEEE Press.
45. Jesmin and Hasan Jamil. “Hypothesis Driven Secondary Network Mining from PubMed using Epiphany.” International Conference on Bioinformatics and Biomedical Technology (ICBBT), IEEE Press, Singapore, April 2009. Pages 483-487. IEEE Press.
46. Shazzad Hosain and Hasan Jamil. “Empowering OWL with Overriding Inheritance, Conflict Resolution and Non-monotonic Reasoning.” Proceedings of the AAAI 2009 Spring Symposium on Social Semantic Web: Where Web 2.0 meets Web 3.0 (AAAI SSSW), Stanford, California, United States, March 2009. Pages 53-58. AAAI Press.
47. Shahriyar Hossain, Munirul Islam, Jesmin and Hasan Jamil. “PhyQL: A Phylogenetic Visual Query Engine.” IEEE Conference on Bioinformatics and BioMedicine (BIBM), Philadelphia, PA. November 2008. Pages 295-298. IEEE Press.
48. Youngju Son, Hasan Jamil and Farshad Fotouhi: “Exploiting Types for Improved Schema Mapping.” In the proceedings of the 2007 ACM Symposium on Applied Computing (SAC), Seoul, Korea. March 2007. Pages 423-429. ACM Press.
49. Youngju Son, Hasan Jamil and Farshad Fotouhi. “Wrapper Induction using Minimal Type System from Web Data”. In the proceedings of the Proceedings of the 2005 Portuguese Conference on Artificial Intelligence". Carlos Bento, Amilcar Cardoso and Gael Dias Editors. Pages130-135. IEEE Press.
50. Avigdor Gal, Giovanni Modica and Hasan Jamil. “OntoBuilder: Fully Automatic Extraction and Consolidation of Ontologies from Web Sources.” In the Proceedings of the 20th IEEE International Conference on Data Engineering (ICDE); Boston, MA. March 30-April 2, 2004. Page 853. IEEE Press.
51. Avigdor Gal, Giovanni Modica and Hasan Jamil. “OntoBuilder: Fully Automatic Extraction and Consolidation of Ontologies from Web Sources.” In the Proceedings of the 22nd International Conference on Conceptual Modeling (ER); Chicago, IL. October 13-16, 2003.
52. Zhijie Guan and Hasan Jamil. “Streamlining Biological Data Analysis using BioFlow.” In the Proceedings of the 3rd IEEE International Symposium on Bioinformatics and Bioengineering (BIBE); Pages 258-262; Washington DC; March 10-12, 2003. IEEE Press.
53. Hasan Jamil. “Implementation of a Least Fixpoint Operator for Fast Mining of Relational Databases.” In the Proceedings of the 2nd International Conference on Data Mining; Pages 633-636 (ICDM), Maebeshi City, Japan; December 9-12, 2002. IEEE Press.
54. Hasan Jamil and Giovanni Modica. “An Object Oriented Extension of XML for Autonomous Web Applications.” In the Proceedings of the 11th ACM International Conference on Information and Knowledge Management (CIKM), Pages 161-168; McLean, VA; November 4-9, 2002. ACM Press.
55. Hasan Jamil and Gillian Dobbie. “A Model Theoretic Semantics for MLS Deductive Databases.” In the Proceedings of the 19th International Conference on Logic Programming (ICLP). LNCS 2401. Pages 130-147; Copenhagen, Denmark; July 29 - August 1, 2002. Springer-Verlag.
56. Hasan Jamil and Rhong Zhou. “SQLⁱ: Towards an Interface Description Language for Relational Databases.” Proceedings of the ACM International Working Conference on Advanced Visual Interfaces (AVI), Pages 251-256; Trento, Italy; May 22-24, 2002. ACM Press.
57. Hasan Jamil. “Ad Hoc Association Rule Mining as SQL3 Queries.” In the Proceedings of the IEEE International Conference on Data Mining (ICDM), Pages 609-612; San Jose, California, November 29 - December 2, 2001. IEEE Press.
58. Hasan Jamil. “Mining First-order Knowledgebases for Association Rules.” In the Proceedings of the Thirteenth IEEE International Conference on Tools with Artificial Intelligence (ICTAI) (one of the best papers of IEEE ICTAI 2001); Pages 218-227; Dallas, Texas; November 7-9, 2001. IEEE Press.
59. Hasan Jamil, Giovanni Modica and Maria Teran. “Towards a Visual Query Interface for Phylogenetic Databases.” In the Proceedings of the 10th ACM International Conference on Information and Knowledge Management (CIKM), Pages 57-64. Atlanta, Georgia, November 5-10, 2001. ACM Press.
60. Liangyou Chen and Hasan Jamil. “Supporting Remote User Defined Functions in Heterogeneous Biological Databases.” In the Proceedings of the 2nd IEEE International Symposium on Bioinformatics and Bioengineering (BIBE), Pages 144-152. Bethesda, Maryland; November 4-6, 2001. IEEE Press.
61. Hasan Jamil, Giovanni Modica and Maria Teran. “Querying Phylogenies Visually.” In the Proceedings of the 2nd IEEE International Symposium on Bioinformatics and Bioengineering (BIBE), Pages 3-10. Bethesda, Maryland; November 4-6, 2001. IEEE Press.
62. Hasan Jamil. “A Basis for Mining First-order Declarative Knowledge.” In the Proceedings of the 14th International Conference on Applications of Prolog (INAP); Pages 30-37; Tokyo, Japan; October 20-22, 2001.
63. Giovanni Modica, Avigdor Gal and Hasan Jamil. “The Use of Machine-Generated Ontologies in Dynamic Information Seeking.” In the Proceedings of the Cooperative Information Systems Conference (CoopIS); Pages 433-448. LNCS 2172. Trento, Italy; September 5-7, 2001. Springer-Verlag.
64. Hasan Jamil. “On the Equivalence of Top-Down and Bottom-Up Data Mining in Relational Databases.” In the Proceedings of the 3rd International Conference on Data Warehousing and Knowledge Discovery (DaWaK) (one of the four best papers of DaWaK 2001); Pages 41-50. LNCS 2114. Munich, Germany, September 5-7, 2001. Springer-Verlag.
65. Jiawei Han, Hasan Jamil, Ying Lu, Y., Liangyou Chen, Yaqin Liao and Jian Pei. “DNA-Miner: A System Prototype for Mining DNA Sequences.” In the Proceedings of the ACM International Conference on the Management of Data (SIGMOD), Santa Barbara, CA. May 21-24, 2001. ACM Press.
66. Hasan Jamil and Giovanni Modica. “A View Selection Tool for Multidimensional Databases.” In the Proceedings of the International Conference on the Industrial and Engineering Applications of Artificial Intelligence and Expert Systems (IEA/AIE), Pages 237-246. LNCS/LNAI 2070. Budapest, Hungary, June 4-7, 2001. Springer-Verlag.
67. Hasan Jamil. “A Case for Parameterized Views and Relational Unification.” In the Proceedings of the ACM International Symposium on Applied Computing (SAC); Pages 275-279; Las Vegas, NV; March 11-14, 2001. ACM Press.
68. Hasan Jamil. “Achieving Interoperability of Genome Databases through Intelligent Web Mediators.” In the Proceedings of the IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE); Pages 118-125; Washington, DC; November 8-10, 2000. IEEE Press.
69. Hasan Jamil. “GQL: A Reasonable Complex SQL for Genomic Databases.” In the Proceedings of the IEEE International Symposium on Bio-Informatics and Biomedical Engineering (BIBE); Pages 50-59; Washington, DC; November 8-10, 2000. IEEE Press.
70. Hasan Jamil. “Declarative Semantics of Belief Queries in MLS Deductive Databases.” In the Proceedings of the Fourteenth Annual IFIP WG 11.3 Working Conference on Database Security (DBSec), Pages 323-328; Schoorl, The Netherlands; August 21-23, 2000. Kluwer Academic Publishers.
71. Hasan Jamil. “A Logic Based Language for Parametric Inheritance.” In the Proceedings of the Seventh International Conference on Principles of Knowledge Representation and Reasoning (KR); Pages 611-622; Breckenridge, CO. April 12-17, 2000. Morgan Kaufmann Publishers.
72. Hasan Jamil. “Belief Reasoning in MLS Deductive Databases.” In the Proceedings of the ACM International Conference on Management of Data (SIGMOD); Philadelphia, PA; Pages 109--120, May 31-June 3, 1999. ACM Press.
73. Hasan Jamil. “Implementing Abstract Objects with Inheritance in Datalog^neg.” In the Proceedings of the 23rd International Conference on Very Large Databases (VLDB); Athens, Greece, Pages 56--65; August, 1997. Morgan Kaufmann Publishers.
74. Hasan Jamil and Laks Lakshmanan. “A Declarative Semantics for Behavioral Inheritance and Conflict Resolution.” John Lloyd Editor; In the Proceedings of the 12th International Logic Programming Symposium (ILPS); Pages 130-144; Portland, Oregon. December 4-7, 1995. AAAI Press.
75. Hasan Jamil and Laks Lakshmanan. “An Object-Oriented Front-end for Deductive Databases.” V. S. Alagar and M. Nivat Editors; In the Proceedings of the 4th International Conference on Algebraic Methodology and Software Technology (AMAST); Pages 581-584; Montreal, Canada. LNCS 936. July 3-7, 1995. Springer-Verlag.
76. Michele Bugliesi and Hasan Jamil. “A Stable Model Semantics for Behavioral Inheritance in Deductive Object Oriented Language.” G. Gottlob and M. Y. Vardi Editors; In the Proceedings of the 5th International Conference on Database Theory (ICDT); Pages 222-237; Prague, Czech Republic; LNCS 893. January 10-13, 1995. Springer-Verlag.
77. Hasan Jamil and Fereidoon Sadri. “Recognizing Credible Experts in Inaccurate Databases.” Z. W. Ras and M. Zemankova Editors; In the Proceedings of the 8th International Symposium on Methodologies for Intelligent Systems (ISMIS); Pages 46-55; Charlotte, North Carolina. LNAI 869. October 16-19, 1994. Springer-Verlag.
78. Michele Bugliesi and Hasan Jamil. “A Logic for Encapsulation in Object Oriented Languages.” M. Hermenegildo and J. Penjam Editors; In the Proceedings of the 6th International Symposium on Programming Language Implementation and Logic Programming (PLILP); Pages 213-229; Madrid, Spain; LNCS 844. September 14-16, 1994. Springer-Verlag.
79. Paul Johannesson and Hasan Jamil. “Semantic Interoperability: Context, Issues, and Research Directions.” In the Proceedings of the 2^nd International Conference on Cooperative Information Systems (CoopIS); Pages 180-191; Toronto, Canada; May 17-20, 1994.
80. Hasan Jamil and Laks Lakshmanan. “ORLog: A Logic for Semantic Object-Oriented Models.” In the Proceedings of the 1st International Conference on Information and Knowledge Management (CIKM), Pages 584-592; Baltimore, Maryland; November, 1992.

Refereed Workshop Publications

1. Mohammad Ashrafuzzaman, Hasan Jamil, Yacine Chakhchoukh and Frederick Sheldon. “A Best-Effort Damage Mitigation Model for Cyber-Attacks on Smart-Grids.” In the proceedings of the 13^th IEEE International Workshop on Security, Trust, and Privacy for Software Applications, Tokyo, Japan. July 23-27, 2018. IEEE Press. In Press.
2. Hasan Jamil. “Mapping Abstract Queries to Big Data Web Resources for On-the-fly Data Integration and Information Retrievals.” IEEE ICDE 10^th International Workshop on Information Integration on the Web (IIWeb). Chicago. March 31, 2014. Pages 62-67. IEEE Press.
3. Carlos Rivero and Hasan Jamil. “On Isomorphic Matching of Large Disk Resident Graphs using an XQuery Engine.” IEEE ICDE 5^th International Workshop on Graph Data Management (GDM). Chicago. March 31, 2014. Pages 20-27. IEEE Press.
4. Hasan Jamil. “Design of Declarative Graph Query Languages: On the Choice between Value, Pattern and Object based Representations for Graphs.” IEEE ICDE 2012 3^rd Workshop on Graph Data Management (GDM). Washington DC. April 5, 2012. Pages 178-185. IEEE Press.
5. Kazi Zakia Sultana, Anupam Bhattacharjee and Hasan Jamil. “EpICS: A System for Analyzing Genome-wide Epistasis and Genetic Variations.” In the Proceedings of the First IEEE International Workshop on Graph Techniques for Biomedical Networks (GTBN); Washington DC. November 1-4, 2009. IEEE Press.
6. Emdad Ahmed and Hasan Jamil. “Post Processing Wrapper Generated Tables for Labeling Anonymous Datasets.” In the Proceedings of the 11th ACM International Workshop on Web Information and Data Management (WIDM); Hong Kong. November 2, 2009. Pages 63-66. ACM Press.
7. Hasan Jamil and Aminul Islam. “The Power of Declarative Languages: A Comparative Exposition of Scientific Workflow Design using BioFlow and Taverna.” In the Proceedings of the IEEE SCC International Workshop on Scientific Workflows (SWF); Los Angeles, CA. Pages 322-329. July 2009. IEEE Press.
8. Shahriyar Hossain and Hasan Jamil. “A Visual Interface for on-the-fly Biological Database Integration and Workflow Design using VizBuilder.” Data Integration in the Life Sciences Workshops, Manchester, UK, July 2009. Pages 157-172. LNCS 5647. Springer-Verlag.
9. Hasan Jamil and Bilal El-Hajj-Diab. “BioFlow: A Web-based Declarative Workflow Language for Life Sciences.” International Workshop on Scientific Workflows (SWF), United States, July 2008. Pages 453-460. IEEE Press.
10. Hong-Cheu Liu, John Zeleznikow and Hasan Jamil. “Logic-based Association Rule Mining in XML Documents”. In the proceedings of the 2006 International Workshop on XML Research and Applications (XRA). LNCS 3842. January 15, 2006. Pages 97-106. Springer-Verlag.
11. Avigdor Gal, Giovanni Modica and Hasan Jamil. “OntoBuilder: Fully Automatic Extraction and Consolidation of Ontologies from Web Sources.” In the Proceedings of the Semantic Integration Workshop, 2nd International Semantic Web Conference (ISWC); Florida. October 20, 2003.
12. Liangyou Chen, Hasan Jamil and Nan Wang. “Automatic Wrapper Generation for Semi-Structured Biological Data Based on Table Structure Identification.” In the Proceedings of the DEXA International Workshop on Biological Data Management (BIDM), Praha, Czech Republic, September 1-5, 2003. Pages 55-59. IEEE Press.
13. Hasan Jamil, Leszek Maciaszek, Mehmet Orgun and Raymond Wong. “Four-tier Mobile Databases – Some Research Implications.” In the Proceedings of the 2nd Australian Workshop on Mobile Computing, Databases & Applications; Melbourne, Australia; November, 1997.
14. Hasan Jamil. “Inheritance with Overriding Without Non-monotonic Reasoning in Datalog⁺⁺.” In the Proceedings of the 5th ICLP International Workshop on Deductive Databases and Logic Programming (DDLP), Leuven, Belgium. Pages 83-100; July, 1997.
15. Hasan Jamil and Fereidoon Sadri. “Trusting an Information Agent.” In the Proceedings of the International Workshop on Rough Sets and Knowledge Discovery (RSKD); Pages 357-365. Banff, Alberta; October, 1993. ISBN 978-3-540-19885-7. Springer-Verlag London.
16. Nematollah Shiri and Hasan Jamil. “Uncertainty as a Function of Expertise.” In the Proceedings of the Workshop on Incompleteness and Uncertainty in Information Systems; Pages 153-166; Montreal, Quebec. October, 1993. ISBN 978-3-540-19897-0. Springer-Verlag London.
17. Hasan Jamil and Laks Lakshmanan. “Realizing ORLog in LDL.” In the Proceedings of the ACM SIGMOD Workshop on Combining Declarative and Object-Oriented Databases. Pages 45-59; Washington DC; May, 1993. ACM Press.

Refereed Poster Presentations

1. Belma Yelbay, Alex Gow and Hasan Jamil. “Ranking Novel Regulatory Genes in Gene Expression Profiles using NetExpress.” ACM Symposium on Applied Computing (SAC). Marrakech, Morocco. Pages 24-27. April 3-7, 2017. ACM Press.
2. Belma Yelbay, Ilker Birbil, Kerem Bulbul and Hasan Jamil. “Approximating the Minimum Hub Cover Problem on Planer Graphs and its Application to Query Optimization.” In the Proceedings of the SIAM Conference on Optimization, San Diego, CA. May 19-22, 2014
3. Hasan Jamil. “MapBase: A Virtual Biological ID Map Database.” In the Proceedings of the 8th International Symposium on Bioinformatics Research and Applications (ISBRA), Dallas, Texas. May 21-23, 2012. Short Abstract. Pages 17-20.
4. Hasan Jamil. “AutoPipe: A Toolbox for Systems Biology Workflow Query Synthesis.” In the Proceedings of the 8th International Symposium on Bioinformatics Research and Applications (ISBRA), Dallas, Texas. May 21-23, 2012. Short Abstract. Pages 1-4.
5. Hasan Jamil. “A Crowdsourcing Model for Annotating and Curating Uncertain Biological Data.” 2012 Biocuration Conference. Washington DC. April 2-4, 2012.
6. Hasan Jamil. “The Role of p53 in Oligodendrocyte UPR.” 9th Annual ISCB Rocky Mountain Bioinformatics Conference, Aspen, Colorado. December 8-10, 2011.
7. Jesmin, S. M. Mahbubur Rashid, Hasan Jamil, Raquel Hontecillas and Josep Bassaganya-Riera. “Understanding the Molecular Mechanism of Type 2 Diabetes (T2D) and Hypertension.” Diabetes UK 2011 Conference, London, UK. March, 2011.
8. Alan A. Dombkowski, Zakia Sultana, Hasan Jamil and Douglas Craig. “Combinatorial microRNA activity associated with breast cancer metastasis is revealed through computational analysis of target genes and pathways.” 2010 American Association for Cancer Research Annual Conference (AACR), Washington DC. April 2010.
9. Aminul Islam and Hasan Jamil. “Curray: A Query Language for Microarray Data Analysis.” In the Proceedings of the 6th International Symposium on Bioinformatics Research and Applications (ISBRA), Storrs, Connecticut. March 2010. Short Abstract. Pages 18-21.
10. Anupam Bhattacharjee, Aminul Islam, Mohammad Shafkat Amin, Shahriyar Hossain, Shazzad Hosain and Hasan Jamil. “LifeDB: An Autonomous Semantic Data Integration System for Life Sciences.” International Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS), Edinburgh, UK, November 2008. Springer-Verlag.
11. Munirul Islam, Shazzad Hosain, Hasan Jamil, Morris Goodman and Derek Wildman. “Phoenix: A Tool for Estimating Species Divergence Times.” Ohio Collaborative Conference on Bioinformatics (OCCB), Toledo, OH. May 2008. Page 34.
12. William Grosky, Farshad Fotouhi, Anthony Aristar, Ming Dong, Hasan Jamil, Shiyong Lu and Robert Reynolds. “A Digital Library for Endangered Languages.” Proceedings of the 2003 Nara Symposium for Digital Silk Roads, Nara, Japan, December 2003, pp. 85-92.
13. Hasan Jamil and Giovanni Modica. “Leveraging Dynamic Inheritance in Complex Ontology Representation.” In the Proceedings of the 10th International Conference on Cooperative Information Systems (CoopIS), Pages 525; Irvine, CA. October 30 - November 1, 2002. Springer-Verlag.
14. Emilia Martins, Susan Alberts, Jane Altmann, Jack Bradbury, Anne Clark, James Ha, Hasan Jamil and Sue Margulis. “EthoSource: Facilitating Access to Behavioral Data.” Evolution 2003 Symposium. Chico, CA. June 20-24, 2003.
15. Giovanni Modica and Hasan Jamil. “Enhancing Reuse via Inheritance in XML.” 11th ACM International Conference on World Wide Web (WWW), Honolulu, HI. May 7-11, 2002. ACM Press.