Chuming ChenChuming Chen, Ph.D.


Assistant Professor
Department of Computer & Information Sciences
University of Delaware

Contact

Office: 205 Delaware Biotechnology Institute

Mailing address:
Delaware Biotechnology Institute
15 Innovation Way, Room 205
University of Delaware
Newark, DE 19711

Phone: (302) 831-3426
FAX: (302) 831-4841
E-Mail: chenc@udel.edu
Web Site: UD CIS Department Profile

Education

Ph.D., Computer Science and Engineering, University of South Carolina, USA, 2008
M.S., Computer Science, University of South Carolina, USA, 2003
Ph.D., Geology, Nanjing University, P. R. China, 2000
B.S., Structural Geology and Geophysics, Nanjing University, P. R. China, 1994

Research Interests

  • Current Topics:

    Automated mass annotation of protein sequences, MS Proteomics Informatics, Omics Data Integration and Meta-analysis, High Performance Computing, Semantic Web, Description Logics, Ontology Engineering, Temporal Database, Network Security.

  • Past Topics:

    Non-destructive Integrity Evaluation in Micro-piles, Petroleum Geology, Structural Geology, Geophysics.

Current Projects

  • Unified Rule Application (URA)

    URA automated annotation project uses UniRules which describe conditional annotation templates (UniRules) to define annotation which can be generated for (selected) predicted features. The goal of this research is to build a system, which can automatically annotate millions of TrEMBL protein sequence entries.

  • Literature Mining of Pathogenesis-Related Proteins in Human Pathogens for Database Annotation

    To develop an automated text mining system to facilitate literature-based curation of pathogenesis-related proteins in pathogens of military relevance.

  • Omics Data Integration

    To develop systematic statistical and computational methods to adequately integrate Omics data to support Meta-analysis of multiple high-throughput biological experiments.

Selected Publications

Wu CH, Chen C. (Editors) (2010). Bioinformatics for Comparative Proteomics. A volume in Series Methods in Molecular Biology. Series Editor: John M. Walker. Humana Press.

Chen C, Matthews MM. (2008). A New Approach to Managing the Evolution of OWL Ontologies. In Proceedings of The 2008 International Conference on Semantic Web and Web Services. Las Vegas, Nevada, USA, p. 57-63.

Chen C, Matthews MM. (2008). Metrics for Evaluating the Semantic Implications of Changes in Evolving Ontologies. In Proceedings of The 2008 International Conference on Semantic Web and Web Services. Las Vegas, Nevada, USA, p.76-82.

Chen C, Matthews MM. (2007). Extending Description Logic for Reasoning about Ontology Evolution. In Proceedings of The 2007 IEEE/WIC/ACM International Conference on Web Intelligence. Silicon Valley, California, USA, p. 452-456.

Huang CT, Matthews MM, Ginley M, Zheng X, Chen C, Chang M. (2007). Efficient and Secure Multicast in WirelessMAN: A Cross-layer Design. Journal of Communications Software and Systems. Vol. 3, No. 3, p. 199-206.

Chen C, Matthews MM. (2007). Extending Description Logic for Reasoning about Ontology Evolution. Technical Report (USC CSE TR-2007-012).

Almeida JS, Chen C, Gorlitsky R, Stanislaus R, Aires-de-Sousa M, Eleuterio P, Carrico J, Maretzek A, Bohn A, Chang A, Zhang F, Mitra R, Mills, GB, Wang X, Deus HF. (2006). Data integration gets 'Sloppy'. Nature Biotechnology, (9):1070-1071.

Stanislaus R, Chen C, Franklin J, Arthur J, Almeida JS. (2005). AGML Central: web based gel proteomic infrastructure Bioinformatics, Vol. 21, 1754-1757.

McKillen DJ, Chen YA, Chen C, Jenny MJ, Trent HF III, Robalino J, McLean DC Jr., Gross PS, Chapman RW, Warr GW, Almeida JS. (2005). Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms. BMC Genomics, 6:34.

Zheng X, Chen C, Huang CT, Matthews MM, Santhapuri N. (2005). A Dual Authentication Protocol for IEEE 802.11 Wireless LANs. In Proceedings of the 2nd International Symposium on Wireless Communication Systems. p. 565-569.

Chen C, Matthews MM. (2004). A Web Interface for Nessus Network Security Scanner. In Proceedings of the International Conference on Internet Computing, Hamid R. Arabnia and Olaf Droegehorn (editors), Las Vegas, Nevada, USA, p. 383-389.


 

Center for Bioinformatics & Computational Biology • 15 Innovation Way • Newark, DE 19711 • USA
Phone: 302-831-0161 • E-mail: bioinformatics@udel.edu

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