Dr. Shiyong Lu's publications


2015

 

1.     Andrey Kashlev, Shiyong Lu, and Artem Chebotko, “Typetheoretic Approach to the Shimming Problem in Scientific Workflows”, IEEE Transactions on Services Computing (TSC), 8(5), pp.795-809, 2015. Impact factor: 2.46. Download.

2.     Yong Zhao, Youfu Li, Ioan Raicu, Shiyong Lu, Cui Lin, Yanzhe Zhang, Wenhong Tian and Ruini Xue, “A Service Framework for Scientific Workflow Management in the Cloud”, IEEE Transactions on Services Computing (TSC), 8(6), pp.930-944, 2015.

3.     Yong Zhao, Youfu Li, Ioan Raicu, Shiyong Lu, Wenhong Tian, and Heng Liu, “Enabling Scalable Scientific Workflow Management in the Cloud”,  Future Generation Computer Systems (FGCS), 46, pp.3-16, Elsevier. Impact factor: 2.639, 2015.

4.     Mahdi Ebrahimi, Aravind Mohan, Andrey Kashlev, and Shiyong Lu, “BDAP: A Big Data Placement Strategy for Cloud-Based Scientific Workflows”, in Proc. of the First IEEE International Conference on Big Data Computing Services and Applications, pp.105-114, San Francisco, USA, 2015. Download.

5.     Aravind Mohan, Mahdi Ebrahimi, Shiyong Lu, “A Folksonomy-Based Social Recommendation System for Scientific Workflow Reuse”, in Proc. Of the IEEE International Conference on Services Computing (SCC), pp.704-711, New York, USA, 2015.

6.     Artem Chebotko, Andrey Kashlev, Shiyong Lu, “A Big Data Modeling Methodology for Apache Cassandra”, IEEE International Congress on Big Data, pp.238-245, New York, USA, 2015. Download. 

7.     Aravind Mohan, Shiyong Lu, and Ke Zhang, “Towards an Online Service for Learning Computational Thinking Using Scientific Workflows”, in Proc. of the IEEE International Conference on Services Computing (SCC), pp.340-347, New York, USA, 2015.

8.     Zaihan Yang, Alexander Kotov, Aravind Mohan and Shiyong Lu, “Parametric and Non-parametric User-aware Sentiment Topic Models”, in Proc. of the 2015 ACM SIGIR Conference, pp.413-422, Santiago, Chile, 2015.

9.     Mahdi Ebrahimi, Aravind Mohan, Shiyong Lu, and Robert Reynolds, “TPS: A Task Placement Strategy for Big Data Workflows”, in Proc. of the 2015 IEEE International Conference on Big Data (IEEE BigData 2015), Santa Clara, CA, U.S.A., 2015.

 

2014

 

10.            Ping Yang, Xing Xie, Indrakshi Ray, Shiyong Lu, “Satisfiability Analysis of Workflows with Control-Flow Patterns and Authorization Constraints”, IEEE Transactions on Services Computing (TSC), 7(2), 237-251, 2014. Impact factor: 2.46. Download.

11.            Jia Zhang, Daniel Kuc, and Shiyong Lu, “Confucius: A Tool Supporting Collaborative Scientific Workflow Composition”, IEEE Transactions on Services Computing (TSC), 7(1), 2-17, 2014. impact factor: 2.46. Download.

12.            Andrey Kashlev and Shiyong Lu, “A System Architecture for Running Big Data Workflows in the Cloud”, in Proc. Of the IEEE International Conference on Services Computing (SCC), pp.51-58, Anchorage, Alaska, USA, 2014. Download.

13.            Aravind Mohan, Shiyong Lu, Alexander Kotov, “Addressing the Shimming Problem for Big Data Scientific Workflows”, in Proc. Of the IEEE International Conference on Services Computing (SCC), pp.347-354, Anchorage, Alaska, USA, 2014. Download.

14.            Hajar Hamidian, Shiyong Lu, Satyendra P. Rana, Farshad Fotouhi, Hamid Soltanian-Zadeh, “Adapting Medical Image Processing Tasks to a Scalable Scientific Workflow System”, IEEE International Congress on SERVICES, pp. 385-392, Anchorage, Alaska, USA, 2014.

15.            Yong Zhao, Youfu Li, Ioan Raicu, Shiyong Lu, Xuan Zhang. "Architecting Cloud Workflow: Theory and Practice", IEEE International Conference on Computer and Information Technology (CIT), pp.466-473, 2014. 

16.            Yong Zhao, Youfu Li, Shiyong Lu, Ioan Raicu, Cui Lin, “Devising a Cloud Scientific Workflow Platform for Big Data”, IEEE International Congress on SERVICES, pp. 393-401, Anchorage, Alaska, USA, 2014.

 

2013

 

17.            Chunhyeok Lim, Shiyong Lu, Artem Chebotko, Farshad Fotouhi, and Andrey Kashlev, “OPQL: Querying Scientific Workflow Provenance at the Graph Level”, Data & Knowledge Engineering (DKE), 88(2013), pp.37-59, 2014. Download. Impact factor: 1.519.

18.            Zijiang Yang, Shiyong Lu, Ping Yang, and, Andrey Kashlev, “Trustworthy and Dynamic Mobile Task Scheduling in Data-Intensive Scientific Workflow Environments”, International Journal of Computers and Their Applications (IJCA), 20(2), pp.65-77, 2013. Download.

19.  Andrey Kashlev, Shiyong Lu, Artem Chebotko: “Coercion Approach to the Shimming Problem in Scientific Workflows”. IEEE SCC 2013:416-423.

20.  Artem Chebotko, John Abraham, Pearl Brazier, Anthony Piazza, Andrey Kashlev, Shiyong Lu: “Storing, Indexing and Querying Large Provenance Data Sets as RDF Graphs in Apache HBase”. IEEE SERVICES 2013:1-8. Download.

 

2012

21.            Xubo Fei and Shiyong Lu, “A Dataflow-Based Scientific Workflow Composition Framework”, IEEE Transactions on Services Computing (TSC), 5(1), pp.45-58, 2012, impact factor: 1.47. Download.

22.            Artem Chebotko, Seunghan Chang, Shiyong Lu, Farshad Fotouhi: Secure XML querying based on authorization graphs. Information Systems Frontiers 14(3): 617-632 (2012). Impact factor: 1.309. Springer. Download.

23.            Jamal Alhiyafi, Shiyong Lu, Jeffrey Ram, “Scientific Workflow Composition in Heterogeneous Environments”, International Journal of Intelligent Information Processing, 3(1), pp.25-36, 2012. Download.

24.            Dong Ruan, Shiyong Lu, Aravind Mohan, Xubo Fei, and Jia Zhang, “A  User-Defined Exception Handling Framework in the VIEW Scientific Workflow Management System”, in Proc. Of the IEEE International Conference on Services Computing (SCC), pp.274-281, Honolulu, Hawaii, 2012. Download.

25.            Ruiqi Luo, Ping Yang, Shiyong Lu, Mikhail Gofman, “Analysis of Scientific Workflow Provenance Access Control Policies”, in Proc. Of the IEEE International Conference on Services Computing (SCC), pp.266-273, Download, Honolulu, Hawaii, 2012.

26.            Xiaoyu Ma, Shiyong Lu, Kai Yang, “Service-Oriented Architecture for SPDFLOW: A Healthcare Workflow System for Sterile Processing Departments”, Proc. Of the IEEE International Conference on Services Computing (SCC), pp.507-514, Honolulu, Hawaii, 2012. Download.

27.            Andrey Kashlev, Artem Chebotko, John Abraham, Pearl Brazier, and Shiyong Lu, "Benchmarking Bottom-Up and Top-Down Strategies for SPARQL-to-SQL Query Translation", in Proc. of the 8th International Conference on Semantic Web and Web Services (SWWS'12), Las Vegas, Nevada, USA, July 16-19, 2012. Download.

 

2011

28.            Dharma Nukarapu, Bin Tang, Liqiang Wang, Shiyong Lu, “Data Replication in Data Intensive Scientific Applications with Performance Guarantee”, IEEE Transactions on Parallel and Distributed Systems (TPDS), 22(8), pp. 1299-1306, 2011. Download

29.            Chunhyeok Lim, Shiyong Lu, Artem Chebotko, and Farshad Fotouhi, “Storing, Reasoning, and Querying OPM-Compliant Scientific Workflow Provenance Using Relational Databases”, Future Generation Computer Systems (FGCS), 27(6), pp.781-789, 2011. Elsevier. Impact factor: 2.229.  Download.

30.            Shiyong Lu and Jia Zhang, “Collaborative Scientific Workflows Supporting Collaborative Science”, International Journal of Business Process Integration and Management, 5(2), pp.185-199, 2011.

31.            Zijiang Yang, Shiyong Lu, Ping Yang, and Fahima Bhuyan, "Model Checking Approach to Secure Host Access Enforcement of Mobile Tasks in Scientific Workflows", International Journal of Computers and Their Applications (IJCA), 18(3), pp.148-159, 2011.

32.            Chunhyeok Lim, Shiyong Lu, Artem Chebotko, and Farshad Fotouhi, “OPQL: A First OPM-Level Query Language for Scientific Workflow Provenance”, in Proc. Of the IEEE International Conference on Services Computing (SCC), pp.136-143, Washington DC, 2011. Download.

33.            Xubo Fei, Shiyong Lu, and Jia Zhang, “A Granular Concurrency Control for Collaborative Scientific Workflow Composition”, in Proc. Of the IEEE International Conference on Services Computing (SCC), pp.410-417, Washington DC, 2011. Download.

34.            Cui Lin and Shiyong Lu, “Scheduling Scientific Workflows Elastically for Cloud Computing”, in Proc. Of the IEEE International Conference on Cloud Computing (CLOUD), pp.746-747, 2011. Download

35.            Cui Lin and Shiyong Lu, “SCPOR: An Elastic Workflow Scheduling Algorithm for Services Computing”, IEEE International Conference on Service-Oriented Computing and Applications (SOCA 2011), pp.1-8, Irvine, CA, USA, 2011 . Download

36.            Yong Zhao, Ioan Raicu, Xubo Fei, and Shiyong Lu, “Opportunities and Challenges in Running Scientific Workflows on the Cloud”, International Conference on Cyber-Enabled Distributed Computing and Knowledge Discovery (CyberC 2011), pp.455-462, 2011. Download.

 

2010

37.            Artem Chebotko, Shiyong Lu, Seunghan Chang, Farshad Fotouhi, and Ping Yang, "Secure Abstraction Views for Scientific Workflow Provenance Querying", IEEE Transactions on Services Computing (TSC), 3(4), pp.322-337, 2010. Download.

38.            Cui Lin, Darshan Pai, Shiyong Lu, Otto Muzik, Jing Hua, “Coclustering for Cross-Subject Fiber Tract Analysis through Diffusion Tensor Imaging”, IEEE Transactions on Information Technology in Biomedicine (TITB), 14(2), pp.514-525, 2010. Impact factor: 1.69. Download

39.            Artem Chebotko, Shiyong Lu, Xubo Fei, and Farshad Fotouhi, “RDFProv: A Relational RDF Store for Querying and Managing Scientific Workflow Provenance”, Data & Knowledge Engineering (DKE), 69(8), pp.836-865, 2010, Elsevier.  Impact factor: 1.745. Download.

40.            Ping Yang, Shiyong Lu, Mikhail I. Gofman, Zijiang Yang, “Information Flow Analysis of Scientific Workflows”, Journal of Computer and System Sciences, 76(6), pp.390-402, 2010, Elsevier. Impact factor: 1.304.

41.            Artem Chebotko and Shiyong Lu, "Nested Optional Join for Efficient Evaluation of SPARQL Nested Optional Graph Patterns", in book "Progressive Concepts for Semantic Web Evolution: Applications and Developments", pp.281-308, Miltiadis Lytras and Amit Sheth (Eds.), Information Science Publishing, ISBN: 160566992X, Feb, 2010.

42.            Xubo Fei and Shiyong Lu, “A Collectional Data Model for Scientific Workflow Composition”, in Proc. of the IEEE International Conference on Web Services (ICWS), pp.567-574, Miami, Florida, USA, July 5-10, 2010. Download.

43.            Jia Zhang, Daniel Kuc, and Shiyong Lu, "Confucius: A Scientific Collaboration System Using Collaborative Scientific Workflows", in Proc. of the IEEE International Conference on Web Services (ICWS), pp.575-583, Miami, Florida, USA, July 5-10, 2010.

44.            Chunhyeok Lim, Shiyong Lu, Artem Chebotko, and Farshad Fotouhi, "Prospective and Retrospective Provenance Collection in Scientific Workflow Environments", in Proc. of the IEEE International Conference on Services Computing (SCC'10), pp.449-456, Miami, Florida, USA, July 5-10, 2010.

45.            Dong Ruan and Shiyong Lu, “Exception Handling in the VIEW Scientific Workflow System”, in Proc. of the IEEE International Conference on Services Computing (SCC), pp.637-638, Miami, Florida, USA, July 5-10, 2010.

 

2009

46.            Cui Lin*, Shiyong Lu, Xubo Fei*, Artem Chebotko*, Darshan Pai, Zhaoqiang Lai, Farshad Fotouhi, and Jing Hua, “A Reference Architecture for Scientific Workflow Management Systems and the VIEW SOA Solution”, IEEE Transactions on Services Computing (TSC), 2(1), pp.79-92, 2009. Download.

47.            Artem Chebotko, Shiyong Lu, and Farshad Fotouhi, “Semantics Preserving SPARQL-to-SQL Translation”, Data and Knowledge Engineering (DKE), 68(10), 973-1000, 2009, Elsevier.  Impact factor: 1.745.

48.            Liqiang Wang, Shiyong Lu, Xubo Fei, Artem Chebotko, H. Victoria Bryant, and Jeffrey L. Ram, “Atomicity and Provenance Support for Pipelined Scientific Workflows”, Future Generation Computer Systems (FGCS), 25(5), pp.568-576, 2009, Elsevier. Impact factor: 2.229. Download.

49.            Jamal Alhiyafi*, Cavitha Sabesan*, Shiyong Lu, and Jeffrey L. Ram, “RECOMBFLOW: A scientific workflow environment for intragenomic gene conversion analysis in bacterial genomes, including the pathogen Streptococcus pyogenes”, International Journal of Bioinformatics Research and Applications (IJBRA), 5(1), pp.1-19, 2009. Download.

50.            Jamal Alhiyafi*, Shiyong Lu, Jeffrey Ram, “Simulation of genomic recombination and the influence of DNA sequence diversity on cluster formation and detectability of recombination: a scientific workflow method”, Int. J. Computational Biology and Drug Design, 2(1), 81-99, 2009. Download.

51.            Jamal Alhiyafi*, Cavitha Sabesan*, Shiyong Lu, and Jeffrey L. Ram, “Association analysis between Intragenomic Gene Conversions and pathogenicity in genomes of Escherichia coli and Shigella spp.: a scientific workflow approach”, International Journal of Functional Informatics and Personalised Medicine (IJFIPM), 2(1), pp.57-76, 2009.  Download.

52.            Cui Lin*, Shiyong Lu, Xubo Fei*, Darshan Pai and Jing Hua, "A Task Abstraction and Mapping Approach to the Shimming Problem in Scientific Workflows", IEEE International Conference on Services Computing (SCC), pp.284-291, Bangalore, India, 2009. Download.

53.            Xubo Fei*, Shiyong Lu, and Cui Lin*, “A MapReduce-Enabled Scientific Workflow Composition Framework”, IEEE International Conference on Web Services (ICWS), pp.663-670, Los Angeles, CA, 2009. Download.

54.            Shiyong Lu and Jia Zhang, “Collaborative Scientific Workflows”, IEEE International Conference on Web Services (ICWS), pp.527-534, Los Angeles, CA, 2009.

 

2008

55.            Ian Foster, Yong Zhao, Ioan Raicu, and Shiyong Lu, “Cloud Computing and Grid Computing 360-Degree Compared”, IEEE Grid Computing Environments, pp.1-10, in conjunction with IEEE/ACM Supercomputing,  Austin, Texas, 2008. Download. (One of the most cited articles in the area of cloud computing.) Download.

56.            Artem Chebotko*, Shiyong Lu, Mustafa Atay, and Farshad Fotouhi, “Efficient Processing of RDF Queries with Nested Optional Graph Patterns in an RDBMS”, International Journal on Semantic Web and Information Systems (IJSWIS), 4(4), pp.1-30, 2008.

57.            Cui Lin*, Shiyong Lu, Xuwei Liang, Jing Hua, and Otto Muzik, “Cocluster Analysis of Thalamo-Cortical Fiber Tracts Extracted from Diffusion Tensor MRI”, International Journal of Data Mining and Bioinformatics, 2(4), pp.342-361, 2008. Download.

58.            Xubo Fei*, Shiyong Lu, Thomas Breithaupt, Jörg D. Hardege, and Jeffrey L. Ram,“Modeling mate-finding behavior of the swarming polychaete, Nereis succinea, with TangoInSilico, a scientific workflow based simulation system for sexual searching”, Invertebrate Reproduction and Development, 52(1-2), pp.69-80, 2008. Download.

59.            Jefferey Ram, Xubo Fei*, Michelle Danaher, Shiyong Lu, Thomas Breithaupt, and Jörg D. Hardege, “Finding females: Pheromone-guided reproductive tracking behavior by male Nereis succinea in the marine environment”, Journal of Experimental Biology, 211(5), 757-765, Feb. 2008.

60.            Claudia Lalancette,  Andrian Platts, Yi Lu, Shiyong Lu, Stephen Krawetz, “Transcription Frameworks of Early Committed Spermatogenic Genes”, Molecular Genetics and Genomics, 280(3):263-74, 2008.

61.            Cui Lin*, Shiyong Lu, Zhaoqiang Lai, Artem Chebotko*, Xubo Fei*, Jing Hua, and Farshad Fotouhi, “Service-Oriented Architecture for VIEW: a Visual Scientific Workflow Management System”, In Proc. of the IEEE 2008 International Conference on Services Computing (SCC 2008), Honolulu, Hawaii, USA, July 2008, pp.335-342.  Download.

62.            Artem Chebotko*, Seunghan Chang*, Shiyong Lu, Farshad Fotouhi, and Ping Yang, “Scientific Workflow Provenance Querying with Security Views”, in Proc. Of the Ninth International Conference on Web-Age Information Management (WAIM 2008), pp. 349-356, Zhangjiajie, P. R. China. IEEE Computer Society Publishing.

63.            Yong Zhao and Shiyong Lu, “A Logic Programming Approach to Scientific Workflow Provenance Querying”, in Proc. of the 2008 International Provenance and Annotation Workshop (IPAW 2008), Salt Lake City, Utah, Lecture Notes in Computer Science, Volume 5272, pp.31-44, 2008.

 

2007

64.            Artem Chebotko*, Mustafa Atay*, Shiyong Lu, and Farshad Fotouhi , “XML Subtree Reconstruction from Relational Storage of XML Documents”, Data and Knowledge Engineering (DKE), 62(2), pp. 199-218, 2007, Elsevier.  Impact factor: 1.745.

65.            Mustafa Atay*, Artem Chebotko*, Dapeng Liu*, Shiyong Lu, Farshad Fotouhi , “Efficient Schema-Based XML-to-Relational Data Mapping”, Information Systems (IS), 32(3), pp.458-476, 2007, Elsevier. Impact factor: 1.966. Download.

66.            Otto Muzik, Diane Chugani, Guangyu Zou, Jing Hua, Yi Lu, Shiyong Lu, Elshi Asano, and Harry Chugani, “Multimodality Data Integration in Epilepsy”, International Journal of Biomedical Imaging (IJBI), Volume 2007, Article ID 13963, 2007.

67.            Artem Chebotko*, Xubo Fei*, Cui Lin*, Shiyong Lu, and Farshad Fotouhi, “Storing and Querying Scientific Workflow Provenance Metadata Using an RDBMS”, in Proc. of the IEEE International Conference on e-Science and Grid Computing (e-Science’07 ), pp.611-618, Bangalore, India, December, 2007. Download.

68.            Ping Yang, Zijiang Yang, and Shiyong Lu, “Formal Modeling and Analysis of Scientific Workflows Using Hierarchical State Machines”, in Proc. of the IEEE International Conference on e-Science and Grid Computing (e-Science’07 ), pp.619-626, Bangalore, India, December, 2007.

69.            Artem Chebotko*, Cui Lin*, Xubo Fei*, Zhaoqiang Lai, Shiyong Lu, Jing Hua, and Farshad Fotouhi, “VIEW: a VIsual SciEntific Workflow management system”, in Proc. of the first IEEE International Workshop on Scientific Workflows (SWF'07), in conjunction with the IEEE 2007 International Conference on Web Services (ICWS’07), pp.207-208, July 9-13, 2007, Salt Lake City, Utah, USA.

70.            Artem Chebotko*, Mustafa Atay*, Shiyong Lu, and Farshad Fotouhi , “Relational Nested Optional Join for Efficient Semantic Web Query Processing”, Guozhu Dong, Xuemin Lin, Wei Wang, Yun Yang, Jeffrey Xu Yu (Eds.), Lecture Notes in Computer Science 4505, pp.428-439, Springer-Verlag 2007, ISBN 978-3-540-72483-4.

71.            Cui Lin*, Shiyong Lu, Danqing Wu, Jing Hua, and Otto Muzik, “Coclustering Based Parcellation of Human Brain Cortex Using Diffusion Tensor MRI Ion I. Mandoiu, Alexander Zelikovsky (Eds.), Lecture Notes in Computer Science 4463, pp. 539-550, Springer-Verlag 2007, ISBN 978-3-540-72030-0.

72.            Mustafa Atay*, Artem Chebotko*, Shiyong Lu, and Farshad Fotouhi, “XML-to-SQL Query Mapping in the Presence of Multi-valued Schema Mappings and Recursive XML Schemas”, Roland Wagner, Norman Revell, Günther Pernul (Eds.), Lecture Notes in Computer Science 4653, pp.603-616, Springer-Verlag 2007, ISBN 978-3-540-74467-2.

73.            Xubo Fei*, Shiyong Lu, Horia F. Pop, and Lily R. Liang, “GFBA: A Biclustering Algorithm for Discovering Value-Coherent Biclusters”, Ion I. Mandoiu, Alexander Zelikovsky (Eds.), Lecture Notes in Computer Science 4463, pp. 1-12, Springer-Verlag 2007, ISBN 978-3-540-72030-0.

74.            Zijiang Yang, Shiyong Lu, and Ping Yang, “Itinerary-based access control for mobile tasks in scientific workflows", in Proc. of the IEEE 21st International Conference on Advanced Information Networking and Applications Workshops - Volume 02, pages 506–511, Niagara Falls, Ontario, Canada, May 2007.

75.            Liqiang Wang, Shiyong Lu, Xubo Fei*, and Jeffrey L. Ram, “A Dataflow-Oriented Atomicity and Provenance System for Pipelined Scientific Workflows”, Yong Shi, G. Dick van Albada, Jack Dongarra, Peter M. A. Sloot (Eds.), Lecture Notes in Computer Science 4489, pp.244-252, Springer-Verlag 2007, ISBN 978-3-540-72587-9. Download.

76.            Seunghan Chang*, Artem Chebotko*, Shiyong Lu, and Farshad Fotouhi, “Graph Matching Based Authorization Model for Efficient Secure XML Querying”, in Proc. of the IEEE 21st International Conference on Advanced Information Networking and Applications Workshops - Volume 02, pp.473-478, Niagara Falls, Ontario, Canada, May 21-23, 2007.

77.            Jamal Alhiyafi*, Cavitha Sebesan*, Shiyong Lu, Melphine Harriott, Deborah Jurczyszyn, Raquel P. Ritchie, Felicitas S. Gonzales, and Jeffrey Ram, “Computational Methods for Analysis of Cryptic Recombination in the Performance of Genomic Recombination Detection Software”, in Proc. of the IEEE 21st International Conference on Advanced Information Networking and Applications Workshops - Volume 01, pp.706-712, May 2007, Niagara Falls Canada. Download.

78.            Cui Lin, Shiyong Lu, Xuena Liang, and Jing Hua, and Otto Muzik, “Genetic cocluster analysis of Thalamo-Cortical Connectivity in Human Brain”, MICWIC, Kellogg Biological Station, 2007.

 

2006

79.            Shiyong Lu, Arthur Bernstein, and Philip Lewis, “Automatic Workflow Verification and Generation”, Theoretical Computer Science (TCS), 353(1-3), pp. 71-92, 2006. Download.

80.            Shiyong Lu, Feng Cao*, and Yi Lu*, “PAMA: a Fast String Matching Algorithm”. International Journal of Foundations of Computer Science (IJFCS), 17(2), pp.357-378, 2006.  Currently ranked as one of the five top accessed articles of the journal, see http://www.worldscinet.com/ijfcs/mkt/top.shtml for more details.

81.            Shiyong Lu, Arthur Bernstein, and Philip Lewis, “Completeness and Realizability: Conditions for Automatic Generation of Workflows”, International Journal of Foundations of Computer Science (IJFCS), 17(1), pp. 223-245, 2006.

82.            Shiyong Lu, Lily R. Liang, Xuena Wang, Yi Lu, Vinay Mandal, Dorrelyn Patacsil, and Deepak Kumar, “FM-test: A Fuzzy-Set-Theory-Based Approach to Differential Gene Expression Data Analysis”, BMC Bioinformatics, 7 (Suppl 4): S7. 2006. (First two authors contributed equally to the paper). Impact factor: 3.43.

83.            Cui Lin*, Shiyong Lu, Xuena Liang, and Jing Hua, “GCA: a Coclustering Algorithm for Thalamo-Cortico-Thalamic Connectivity Analysis”, in Proc. of the IEEE International Workshop on Data Mining in Bioinformatics (DMB’2007), pp.163-168, Hong Kong, December, 2006. Acceptance rate: 27%.

84.            Yi Lu*, Shiyong Lu, Adrian Platts, and Stephen Krawetz, “Mining Correlation between Motifs and Gene Expression”, in Proc. of the IEEE International Conference on Data Mining (ICDM’2006), pp.986-990, Hong Kong, December, 2006. Acceptance rate: 19.6%.

85.            Artem Chetbotko*, Shiyong Lu, Farshad Fotouhi, and Anthony Aristar, “Ontology-based Annotation of Multimedia Language Data for the Semantic Web”, in book “Semantic Web-Based Information Systems: State-of-the-Art Applications”, Amit Sheth and Miltiadis Lytras (Eds.), Cybertech Publishing, ISBN 1599044269, November, 2006.

86.            Zijiang Yang, Shiyong Lu, and Ping Yang, “Runtime Security Verification for Itinerary-Driven Mobile Agents”, in Proc. of the 2nd IEEE International Symposium on Dependable, Autonomic and Secure Computing (DASC'06), pp.177-186, at Indiana University, Purdue University, Indianapolis, USA, September 29-October 1, 2006.

87.            Yi Lu*, Shiyong Lu, Lily R. Liang, and Deepak Kumar, “FM-test: A Fuzzy Set Theory Based Approach to Discovering Diabetes Genes”, in Proc. of the IEEE International Symposium of Computations in Bioinformatics and Bioscience (SCBB’06), pp.48-55, Hangzhou, Zhejiang, China, June, 2006.

88.            Lily R. Liang, Shiyong Lu, Yi Lu*, Puneet Dhawan, and Deepak Kumar, “CM-test: An Innovative Divergence Measurement and Its Application in Diabetes Gene Expression Data Analysis”, in Proc. of the IEEE International Conference on Granular Computing (GrC’06), Atlanta, pp.262-268, GA, USA, May, 2006. Acceptance rate: 15%.

89.            Yi Lu*, Shiyong Lu, Farshad Fotouhi, Yan Sun, Zijiang Yang, and Lily R. Liang, “PDC: Pattern Discovery with Confidence in DNA Sequences”, in Proc. of the IASTED International Conference on Advances in Computer Science and Technology, pp.345-350, Puerto Vallarta, Mexico, 2006.

90.            Yi Lu*, Shiyong Lu, and Jeffrey Ram, “Fast Search in DNA Sequence Databases Using Punctuation and Indexing”, in Proc. of the IASTED International Conference on Advances in Computer Science and Technology, pp.351-356, Puerto Vallarta, Mexico, 2006. Download.

 

2005

91.            Shiyong Lu, Yezhou Sun, Mustafa Atay and Farshad Fotouhi, “On the Consistency of XML DTDs”, Data and Knowledge Engineering (DKE), 52(2), pp.231-247, 2005.

92.            Artem Chebotko, Yu Deng, Shiyong Lu, Farshad Fotouhi, Anthony Aristar, “An Ontology-Based Multimedia Annotator for the Semantic Web of Language Engineering”. Int. J. Semantic Web Inf. Syst. 1(1): 50-67, 2005.

93.            Farhad Mostowfi, Farshad Fotouhi, Shiyong Lu and Anthony Aristar, “LINGOES: A Linguistic Ontology Management System”, International Journal of Digital Information Management, 3(4), pp. 231-234, December 2005.

94.            Darshan Pai, Jiafeng Jiang, Jing Hua, Ye Duan, Otto Muzik, and Shiyong Lu, “3D Segmentation of Brain Structures Using PDE-Driven Surface Growing”. In Proc. of the 2005 NAFIPS Annual Conference on Soft Computing for Real World Applications, Ann Arbor, MI, USA, June 2005.

95.            Shiyong Lu and Cheng-zhong Xu, “A Formal Framework for Mobile Agent Itinerary Specification, Safety Reasoning, and Logic Analysis”, in Proc. of the 3rd IEEE International Workshop on Mobile Distributed Computing (MDC’05), in conjunction with ICDCS’2005, Columbus, OH, USA, 2005.

96.            Artem Chebotko*, Dapeng Liu*, Mustafa Atay*, Shiyong Lu, and Farshad Fotouhi, “Reconstructing XML Subtrees from Relational Storage of XML Documents”, in Proc. of the 2nd International Workshop on XML Schema and Data Management (XSDM’05), in conjunction with ICDE’2005, Tokyo, Japan, April, 2005.

97.            Chunxia Zhang*, Shiyong Lu, and Lily R. Liang. “MetaFinder: a Meta-Search Engine with an Open Architecture”, in Proc. of the 20th International Conference on Computers and Their Applicaitons (CATA’2005), New Orleans, Louisiana, USA. March 2005.

 

2004

98.            Shiyong Lu, Arthur Bernstein, and Philip Lewis, “Correct Execution of Transactions at Different Isolation Levels”, IEEE Transactions on Knowledge and Data Engineering (TKDE). 16(9), pp. 1070-1081, September 2004. 

99.            Yi Lu*, Shiyong Lu, Farshad Fotouhi, Youping Deng, and Susan Brown, “Incremental Genetic K-means Algorithm and its Application in Gene Expression Data Analysis”, BMC Bioinformatics, 5(172), 2004. Impact factor: 3.43. Download.

100.       Shiyong Lu, Rong Huang*, Artem Chebotko*, Yu Deng*, and Farshad Fotouhi, “ImageSpace: An Environment for Image Ontology Management”, International Journal of Information Theories and Applications, 11(2), pp. 127-134, 2004.

101.       Shiyong Lu, Dapeng Liu*, Farshad Fotouhi, Ming Dong, Robert Reynolds, Anthony Aristar, Martha Ratliff, Geoff Nathan, Joseph Tan, and Ronald Powell, “Language Engineering for the Semantic Web: a Digital Library for Endangered Languages”, Information Research, 9(3), April, 2004.

102.       Ziyang Duan, Arthur Bernstein, Philip Lewis, and Shiyong Lu, “Semantics Based Verification and Synthesis of BPEL4WS Abstract Processes”, in Proc. of the IEEE International Conference on Web Services (ICWS 2004), pp. 734-737, San Diego, CA, USA, July, 2004. Download.

103.       Ziyang Duan, Arthur Bernstein, Philip Lewis, and Shiyong Lu, “A Model for Abstract Process Specification, Verification and Composition”, in Proc. of the Second ACM International Conference on Service Oriented Computing (ICSOC 2004), pp. 232-241, New York City, NY, USA, November, 2004. Download.

104.       Yi Lu*, Shiyong Lu, Farshad Fotouhi, Youping Deng, and Susan Brown, “FGKA: A Fast Genetic K-means Algorithm”, in Proc. of the 19th ACM Symposium on Applied Computing, pp. 162-163, Nicosia, Cyprus, March, 2004. Download.

105.       Artem Chebotko*, Yu Deng*, Shiyong Lu, Farshad Fotouhi, Hennie Brugman, Alexander Klassmann, Han Sloetjes, Albert Russel, and Peter Wittenburg, “OntoELAN: An Ontology-based Linguistic Multimedia Annotator”, in Proc. of the IEEE Sixth International Symposium on Multimedia Software Engineering (MSE’2004), pp. 329-336, Miami, FL, USA, December, 2004.

106.       Mustafa Atay*, Yezhou Sun*, Dapeng Liu*, Shiyong Lu, and Farshad Fotouhi, “Mapping XML Data to Relational Data: a DOM-based Approach”, in Proc. of the 8th IASTED International Conference on Internet and Multimedia Systems and Applications (IMSA’2004), pp. 59-64, Kauai, Hawaii, USA. August 2004.

107.       Lei Chen*, Shiyong Lu, and Jeffrey Ram, “Compressed Pattern Matching in DNA Sequences”, in Proc. of the IEEE Computational Systems Bioinformatics Conference (CSB'2004), pp. 62-68, Stanford, CA, USA, August 2004.  Acceptance rate: 15%. Download.

108.       Artem Chebotko, Shiyong Lu, Farshad Fotouhi, “Challenges for Information Systems Towards the Semantic Web”, AIS SIGSEMIS Semantic Web and Information Systems Newsletter, Volume 1, Number 1, pp. 26-28, April, 2004. Full Bulletin.

109.       Shiyong Lu, Rong Huang*, and Farshad Fotouhi, “Annotating Linguistic Data with ImageSpace for the Preservation of Endangered Languages”, in Proc. of the 19th International Conference on Computers and Their Applications (CATA'2004), pp. 193-196, Seattle, WA, USA, March, 2004.

110.       Rong Huang*, Shiyong Lu, and Farshad Fotouhi, “ImageSpace: An Image Ontology Creation and Annotation Tool”, in Proc. of the 19th International Conference on Computers and Their Applications (CATA'2004), pp. 340-343, Seattle, WA, USA, March, 2004.

111.       Manjeet Rege*, Izabell Caraconcea*, Shiyong Lu, and Farshad Fotouhi, “Querying XML Documents from a Relational Database in the Presence of DTDs”, Lecture Notes in Computer Science, Volume 3347, pp. 168-177, R. K. Ghosh and Hrushikesha Mohanty (Eds.), Springer-Verlag, ISBN 3-540-24075-6, 2004.

 

2003

112.       Shiyong Lu, Yezhou Sun*, Mustafa Atay*, and Farshad Fotouhi, “A New Inlining Algorithm for Mapping XML DTDs to Relational Schemas”, Lecture Notes in Computer Science, Volume 2814, pp. 366-377, Manfred A. Jeusfeld and Oscar Pastor (Eds.), Springer-Verlag, ISBN 3-540-20257-9, 2003. Download.

113.       Jeffrey Stefan, Robert Reynolds, Farshad Fotouhi, Anthony Aristar, Shiyong Lu, and Ming Dong, "Evolution Based Approaches to the Preservation of Endangered Natural Languages", in Proc. of the IEEE International Congress on Evolutionary Computation (CEC'2003), pp. 1980-1987, Canberra, Australia, December, 2003.

114.       William I. Grosky, Farshad Fotouhi, Anthony Aristar, Shiyong Lu, Ming Dong, and Robert Reynolds, “A Digital Library for Endangered Languages”, the Nara Symposium for Digital Silk Roads (DSR), Nara, Japan, December, 2003.

115.       Subhra Bose, Ziyang Duan, and Shiyong Lu, “An XML-based Framework for Rapid Development of Interoperable Trading Systems”, in Proc. of the 7th IASTED International Conference on Software Engineering and Applications (SEA'2003), pp. 184--189, Marina del Rey, CA, USA, November 2003.

116.       Zongmin Ma*, Shiyong Lu, and Farshad Fotouhi, “Conceptual Data Models for Engineering Information Modeling and Formal Transformation of EER and EXPRESS-G”, Lecture Notes in Computer Science, Volume 2813, pp. 573-575, Il-Yeol Song, Stephen W. Liddle, Tok Wang Ling and Peter Scheuermann (Eds.), Spinger-Verlag, ISBN 3-540-20299-4, 2003.

117.       Shiyong Lu, Yezhou Sun*, Mustafa Atay*, and Farshad Fotouhi, “A Sufficient and Necessary Condition for the Consistency of XML DTDs”, Lecture Notes in Computer Science, Volume 2814, pp. 250-260, Manfred A. Jeusfeld and Oscar Pastor (Eds.), Spinger-Verlag, ISBN 3-540-20257-9, 2003.

118.       Farshad Fotouhi, Shiyong Lu, Ming Dong and Michael Johnson, “Deriving Ontologies from Image Databases”, International Workshop on Annotation and Resource Discovery of Geographic Image Data, Nikko, Japan, March, 2003.

119.       Shuyun Xu, Yu Li, and Shiyong Lu, “ERDraw: an XML-based ER-diagram Drawing and Translation Tool”, in Proc. of the 18th International Conference on Computers and Their Applications (CATA’2003), pp. 143-146, Honolulu, Hawaii, USA, March, 2003.

120.       Farshad Fotouhi, Shiyong Lu, Ming Dong and Michael Johnson, “Deriving Ontologies from Web Documents”, International Symposium on Digital Silk Roads (DSR), Hawaii, USA, March, 2003.  

 

1999-2002

121.       Shiyong Lu, “Semantic Correctness of Transactions and Workflows”, Ph.D. dissertation, Stony Brook University, 2002. Advisor: Arthur J. Bernstein. Download.

122.       Shiyong Lu, Ming Dong and Farshad Fotouhi, “The Semantic Web: Opportunities and Challenges for Next-Generation Web Applications”, Information Research, 7(4), 2002. Download.

123.       Arthur J. Bernstein, Philip M. Lewis, and Shiyong Lu, “Semantic Conditions for Correctness at Different Isolation Levels”, in Proc. of the 16th IEEE International Conference on Data Engineering  (ICDE 2000), pp. 57--66, San Diego, CA, USA, February 28 - March 3, 2000. Download

124.       Shiyong Lu and Scott Smolka, “Model Checking the Secure Electronic Transaction (SET) Protocol”, in Proc. of the 7th IEEE International Symposium on Modeling, Analysis and Simulation of Computer and Telecommunication systems (MASCOTS’1999), pp. 358-365, University of Maryland, College Park, MD, USA, October, 1999. Download.

125.       Shiyong Lu and Steven Skiena, “Filling a Penny Album”, Chance, 13(29), pp. 25-28, 2000.

126.       Ziyang Duan, Albert Loo, Biswajit Sarkar, Shiyong Lu, Mark Van Loon and Subhra Bose, “A Structured Approach to Trade Negotiation Applications”, in Proc. of the 15th International Conference on Computer Applications in Industry and Engineering (CAINE’2002), pp. 162—165, San Diego, CA, USA, November, 2002.