Education

Employment

• December 2008 - present Research Assistant Professor
  Department of Computer and Information Sciences, Delaware Biotechnology Institute, University of Delaware, Newark DE, USA
• January 2007 - December 2008 Systems Support, Research Assistant, Instructor
  Department of Computer Science and Engineering, University of South Carolina, Columbia SC, USA
• May 2004 - December 2006 Systems Programmer
  Department of Biostatistics, Bioinformatics and Epidemiology, NHLBI Proteomics Center, Medical University of South Carolina, Charleston SC, USA
• March 2003 - May 2004 Systems Support, Research Assistant
  Department of Computer Science and Engineering, University of South Carolina, Columbia SC, USA
• August 2001 - December 2002 Teaching Assistant
  Department of Computer Science and Engineering, University of South Carolina, Columbia SC, USA
• August 2000 - August 2001 Research Assistant
  Department of Civil Engineering, University of South Carolina, Columbia SC, USA

Research Interests

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 (Full List)

• Bioinformatics for Comparative Proteomics

  Cathy H. Wu and Chuming Chen (Editors)
  A volume in Series Methods in Molecular Biology. Series Editor: John M. Walker. Humana Press. (2010 - in progress)

• Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-throughput "omics" Data

  Chuming Chen, Peter B. McGarvey, Hongzhan Huang and Cathy H. Wu
  Advances in Bioinformatics. (Under review)

• The Universal Protein Resource (UniProt) in 2010

  The UniProt Consortium
  Nucleic Acids Res. 2009, Oct 20 [Epub ahead of print] (2009)

• A New Approach to Managing the Evolution of OWL Ontologies

  Chuming Chen and Manton M. Matthews
  In Proceedings of The 2008 International Conference on Semantic Web and Web Services. Las Vegas, Nevada, USA, p. 57-63. (2008)

• Metrics for Evaluating the Semantic Implications of Changes in Evolving Ontologies

  Chuming Chen and Manton M. Matthews
  In Proceedings of The 2008 International Conference on Semantic Web and Web Services. Las Vegas, Nevada, USA, p.76-82. (2008)

• Extending Description Logic for Reasoning about Ontology Evolution

  Chuming Chen and Manton M. Matthews
  In Proceedings of The 2007 IEEE/WIC/ACM International Conference on Web Intelligence. Silicon Valley, California, USA, p. 452-456. (2007)

• Efficient and Secure Multicast in WirelessMAN: A Cross-layer Design

  Chin-Tser Huang, Manton M. Matthews, M. Ginley, Xinliang Zheng, Chuming Chen, Morris Chang
  Journal of Communications Software and Systems. Vol. 3, No. 3, p. 199-206. (2007)

• Extending Description Logic for Reasoning about Ontology Evolution

  Chuming Chen and Manton M. Matthews
  Technical Report (USC CSE TR-2007-012). (2007)

• Data integration gets 'Sloppy'

  Jonas S. Almeida, Chuming Chen, Robert Gorlitsky, Romesh Stanislaus, Marta Aires-de-Sousa, Pedro Eleuterio, Joao. Carrico, Antonio Maretzek, Andreas Bohn, Allen Chang, Fan Zhang, Rahul Mitra, Gordon B. Mills, Xiaoshu Wang, Helena F. Deus
  Nature Biotechnology, (9):1070-1071. (2006)

• AGML Central: web based gel proteomic infrastructure

  Romesh Stanislaus, Chuming Chen, Jennifer Franklin, John Arthur, and Jonas S. Almeida
  Bioinformatics, Vol. 21, 1754-1757. (2005)

• Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms

  David J. McKillen, Yian A. Chen, Chuming Chen, Matthew J. Jenny, Harold F. Trent III, Javier Robalino, David C. McLean Jr., Paul S. Gross, Robert W. Chapman, Gregory W. Warr and Jonas S. Almeida
  BMC Genomics, 6:34. (2005)

• A Dual Authentication Protocol for IEEE 802.11 Wireless LANs

  Xinliang Zheng, Chuming Chen, Chin-Tser Huang, Manton M. Matthews, Naveen Santhapuri
  In Proceedings of the 2nd International Symposium on Wireless Communication Systems. p. 565-569. (2005)

• A Web Interface for Nessus Network Security Scanner

  Chuming Chen and Manton M. Matthews
  In Proceedings of the International Conference on Internet Computing, Hamid R. Arabnia and Olaf Droegehorn (editors), Las Vegas, Nevada, USA, p. 383-389. (2004)

Professional Memberships

• Professional member of Association for Computing Machinery (ACM)
• Professional member of Institute of Electrical and Electronics Engineers (IEEE)
• Professional member of International Society for Computational Biology (ISCB)

Professional Activities

• Program committee of BIOCOMP'09 (The 2009 International Conference on Bioinformatics and Computational Biology)
• Program committee of PDPTA'09 (The 2009 International Conference on Parallel and Distributed Processing Techniques and Applications)
• Program committee of SWWS'09 (The 2009 International Conference on Semantic Web and Web Services)

Reviewer

• Journal
  • IEEE Transactions on Information Technology in BioMedicine
  • BMC Bioinformatics
  • Journal of Supercomputing
  • International Journal of Information Retrieval Research (IJIRR)
• Conference
  • NDT 2009 (The First International Conference on 'Networked Digital Technologies')

Oral Conference Presentations

• (07/2008) A New Approach to Managing the Evolution of OWL Ontologies at The 2008 International Conference on Semantic Web and Web Services (SWWS'04)
• (07/2008) Metrics for Evaluating the Semantic Implications of Changes in Evolving Ontologies at The 2008 International Conference on Semantic Web and Web Services (SWWS'04)
• (11/2007) Extending Description Logic for Reasoning about Ontology Evolution at The 2007 IEEE/WIC/ACM International Conference on Web Intelligence (WI'07)
• (06/2004) A Web Interface for Nessus Network Security Scanner at The 2004 International Conference on Internet Computing (ICOMP'04)

Invited Talk

• (09/2008) Scalable and Efficient Management Framework for Large-scale OWL Ontologies at Protein Information Resource (PIR), Georgetown University Medical Center

Awards

• Dean's Travel Grant, University of South Carolina, USA, 2008
• Graduate Assistantship, University of South Carolina, USA, 2007-2008
• Student Research Day, Bioinformatics Award, 1st place, Medical University of South Carolina, USA, 2004
• Graduate Assistantship, University of South Carolina, USA, 2000-2004
• Guanghua Scholarship, Nanjing University, P. R. China, 1993
• Outstanding Undergraduate Scholarship, Nanjing University, P. R. China, 1991-1994

Teaching Experience

• Instructor: CSCE350 (Data Structures and Algorithms)

• Teaching Assistant:
  • CSCE747 (Software Testing and Quality Assurance)
  • CSCE520 (Database System Design)

• Instructor: CSCE102 (General Applications Programming)

• Teaching Assistant:
  • CSCE520 (Database System Design)
  • CSCE311 (Operating Systems)

Professional Skills and Knowledge

• Operating Systems

  Linux (Redhat 8, 9, ES 3, 4; Fedora Core 2, 3, 4, 5, 6; Slackware 11, 12; Ubuntu 6,7), Unix (Solaris 8, 9, 10), Windows (Vista, XP, server 2003, 2000), Mac Darwin 9.1.0, Leopard 10.5

• Hardware

  Sun Enterprise E450/E220/T5220, SunFire 280R, Sunray, Sun Ultra 10/80, Sun Blade 150, Dell PowerEdge 2450/2650/2950/4600/6400, PowerVault 122T, HP ProLiant BL20p G2 Server Blade, HP ProLiant DL380 G3, HP StorageWorks 4400, iMac

• System Administration (Solaris: expert 3 years; Linux: expert 4 years)

  System installation (jumpstart), backup and recovery (Veritas Netbackup, CA ARCServe Backup, rdiff-backup); Patch updates; DNS, NIS, NFS, YP, Web server (Apache), Mail Server (Postfix, sendmail), Samba, CVS server configuration and maintenance; Network monitor (Nmap, Nessus, Big Brother), Install and manage PHP and Java based web applications. Maintain MySQL, Oracle database servers

• Programming Languages

  C (Intermediate 2 years, last used 2001), C++ (Intermediate 1 year, last used 2002), C# (Expert 2 years, last used 2004), VB.NET (Expert 2 year, last used 2003), ASP.NET (Intermediate 1 year, last used 2003), Java (Expert 7 years, current), Perl (Expert 2 years, last used 2006), PHP (Expert 2 years, last used 2006), Shell (Expert 4 years, current), Matlab (Intermediate 1 year, last used 2006)

• Networks

  TCP/IP Suite, 802.11 Wireless protocols, Intranet and Internet routing

• Network Security

  DES, AES, RSA, SHA1, Nonce, IPSec, Nessus, Nmap, SSL/TLS, Firewall, PKI

• IDE

  MS Visual Studio .NET, MS Visual Studio 6.0 (MFC), Eclipse, Netbeans, JBuilder, WebSphere, OptimalJ, SunOne Studio, Qt, Rational Rose, JADE, ArcView GIS, LabView, Dreamweaver

• Web Technologies

  Apache, Tomcat, JBoss, IIS, HTML, CSS, JavaScript, DHTML, XML, WSDL, SOAP, UDDI, DAML, RDF, OWL, Jena, OWLAPI, Pellet OWL-DL reasoner

• Database

  MySQL, PostgreSQL, Oracle, SQL server, MS Access, CA Ingres, UML, ER, EER for relational database modeling