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

• Bioinformatics Optimization for Recombinant Protein Expression
  The goal of this project is to develop bioinformatics approaches to improve recombinant protein expression in the plant-based transient expression system.
  
  
• Peptide Match
  Find exact match for one or a batch of peptide sequence query in the UniProtKB database. The search can be performated against the whole UniProtKB sequences or a subset of sequences belonging to an organism from the UniProt complete proteomes. The batch match results can be downloaded for further analysis.
  
  
• UniProt Representative Proteomes
  Representative Proteomes (RPs), are proteomes that are selected from Representative Proteome Groups (RPGs) containing similar proteomes calculated based on co-membership in UniRef50 clusters. Representative Proteome is the proteome that can best represent all the proteomes in its group in terms of the majority of the sequence space and information. RPs at 75%, 55%, 35% and 15% co-membership threshold are provided to allow users to decrease or increase the granularity of the sequence space based on their requirements (Chen et al., 2011). Representative genomes (RGs) are also constructed based on the corresponding RPs.
  
  
• 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.
  
  
• 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.
  
  

Completed Projects

• Transcriptome Analysis of Adipose Tissues in Fat and Lean Line Chickens by RNA-Seq
  The aim of the study is to greatly expand our knowledgebase of the chicken's transcriptome by deep massively parallel RNA sequencing (RNA-Seq) of adipose tissues to identify differentially expressed genes (DEGs) in fully fed and fasted FL and LL chickens at 7 wk of age. To the best of our knowledge, this is the first description of the comprehensive picture of chicken Adipose transcriptome using RAN-Seq technology.
  
  
• ISCU Myopathy Microarray Project
  Performing microarray analysis (R and Bioconductor) on ISCU myopathy biopsies with a two-pronged goal of identifying known and novel genes that might contribute to mitochondrial overload, and identifying transcription factors that mediate the transcriptional response to mis-regulated mitochondrial iron homeostasis.
  
  
• Trimming and de novo Assembly of Illimina High-throughput Short-read
  Studying the trimming of NGS data (quality trimming, adapter trimming, ambigutiy trimming, length trimming etc) and assess their impacts on the quality of de novo assembly.
  
  
• NECC Cyber-Enable Research Project
  Supporting next generation sequencing data analysis and functional interpretation for dogfish shark genome and workforce development.
  
  
• Bacterial Pathogen Diagnostics
  Given a set of nucleotide sequences, sequence analysis approach is used to identify the presence of any Category A bacterial pathogen proteins and identify the bacterial species of the host DNA.
  
  
• aCGH analysis of CNVs in chickens
  Detecting of DNA Copy Number Variation in chickens divergently selected for fatness or leanness and high or low growth by array comparative genomic hybridization (aCGH) method on Roche Nimblegen 385K tiling arrays.
  
  
• 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.
  
  

Selected Publications (Full List) (My profile at Google scholar)

• Update on activities at the Universal Protein Resource (UniProt) in 2013

  The UniProt Consortium
  Nucl. Acids Res. 41 (D1): D43-D47 (2013)

• Aberrant iron homeostasis, oxidative fiber enrichment, and activation of ketogenesis in muscle tissue of ISCU Myopathy patients

  Crooks, Daniel R.; Natarajan, Thanemozhi G.; Chuming Chen; Hongzhan Huang; Ghosh, Manik C.; Wing-Hang Tong; Haller, Ronald G.; Wu, Cathy; Rouault, Tracey A.
  BMC Proceedings, 6(Suppl 3):P58 doi:10.1186/1753-6561-6-S3-P58 (2012)

• Community annotation and bioinformatics workforce development in concert - Little skate genome annotation workshops and jamborees

  Qinghua Wang, Cecilia N. Arighi, Benjamin L. King, Shawn W. Polson, James Vincent, Chuming Chen, Hongzhan Huang, Brewster F. Kingham, Shallee T. Page, Marc Farnum Rendino, W. Kelley Thomas, Daniel W. Udwary, Cathy H. Wu and the North East Bioinformatics Collaborative Curation Team
  Database, doi: 10.1093/database/bar064 (2012)

• Representative Proteomes and Genomes: A standardized, stable and unbiased set of proteomes/genomes ideal for use in genome annotation, metagenomic efforts and analyzing taxonomic nomenclature biases.

  Mona Motwani, Chuming Chen, Hongzhan Huang, Darren Natale, Jamal Theodore, Cathy H. Wu, Raja Mazumder International Biocuration Conference 2012,April 2-4, 2012.

• Community annotation and bioinformatics workforce development in concert - Little skate genome annotation workshops and jamborees

  Qinghua Wang, Cecilia N. Arighi, Benjamin L. King, Shawn W. Polson, James Vincent, Chuming Chen, Hongzhan Huang, Brewster F. Kingham, Shallee T. Page, Marc Farnum Rendino, W. Kelley Thomas, Daniel W. Udwary, Cathy H. Wu and the North East Bioinformatics Collaborative Curation Team
  International Biocuration Conference 2012,April 2-4, 2012.

• Search for genomic footprints of divergent selection from whole genome sequencing of four experimental lines of broiler chickens

  Behnam Abasht, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Michel J. Duclos, Elisabeth LeBihan-Duval, Jean Simon and Larry A. Cogburn
  Plant and Animal Genome XX Program, January 14-18, 2012.

• Reorganizing the protein space at the Universal Protein Resource (UniProt)

  The UniProt Consortium
  Nucl. Acids Res. first published online November 18, 2011 doi:10.1093/nar/gkr98

• UniProt Knowledgebase: a hub of integrated protein data

  Michele Magrane and UniProt Consortium
  Database, Vol. 2011 published online March 29, 2011, doi:10.1093/database/bar009 (2011)

• Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation

  Chuming Chen, Darren A Natale, Robert D Finn, Hongzhan Huang, Jian Zhang, Cathy H Wu, Raja Mazumder
  PLoS ONE, 6(4): e18910. doi:10.1371/journal.pone.0018910 (2011)

• Bioinformatics for Comparative Proteomics

  Cathy H. Wu and Chuming Chen (Editors)
  Methods in Molecular Biology, Vol. 694. John M. Walker (Series Editor). Humana Press. ISBN: 978-1-60761-976-5 (2011)

• Protein Bioinformatics Databases and Resources

  Chuming Chen, Hongzhan Huang and Cathy H. Wu
  In Methods in Molecular Biology, Vol. 694. Cathy H. Wu and Chuming Chen (Editors), John M. Walker (Series Editor). Humana Press. (2011)

• Ongoing and future developments at the Universal Protein Resource

  The UniProt Consortium
  Nucl. Acids Res. 39(Database issue):D214-9. Epub 2010 Nov 4 (2011).

• From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase

  Ursula Hinz and The UniProt Consortium
  Cell Mol Life Sci. April, 67(7): 1049-1064. (2010)

• 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. Volume 2010, Article ID 423589, 19 pages. doi:10.1155/2010/423589. (2010)

• The Universal Protein Resource (UniProt) in 2010

  The UniProt Consortium
  Nucleic Acids Res. 2010 Jan;38(Database issue):D142-8. Epub 2009 Oct 20.

• 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)

Teaching Experience

• Instructor: Transcriptome Assembly (Lecture, Exercise), Expression Analysis (Exercise)

• Instructor: De Novo Assembly of High-throughput Short Read Sequences

• 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 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 IEEE-BIBE-2012 (IEEE International Conference on Bioinformatics and Bioengineering 2012)
• Program committee of IEEE-BIBE-2010 (IEEE International Conference on Bioinformatics and Bioengineering 2010)
• 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
  • Bioinformatics
  • BMC Bioinformatics
  • IEEE Transactions on Information Technology in BioMedicine
  • International Journal of Information Retrieval Research (IJIRR)
  • Journal of Supercomputing
  • PLoS One
  • Biotechnology and Bioengineering
• Conference
  • IEEE-BIBE-2012 (IEEE International Conference on Bioinformatics and Bioengineering 2012)
  • IEEE-BIBE-2010 (IEEE International Conference on Bioinformatics and Bioengineering 2010)
  • 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)

Poster Conference Presentations

• (03/2010) Detection of DNA Copy Number Variation in Chickens Divergently Selected for Fatness or Leanness and High or Low Growth at X-gen Congress & Expo 2010

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

Professional Skills and Knowledge

• Operating Systems

  Linux (Redhat 8, 9, ES 3, 4, 5; Fedora Core 2, 3, 4, 5, 6, 13; Slackware 11, 12; Ubuntu 6,7; Gentoo 10; 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 4 years; Linux: expert 6 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 9 years, current), Perl (Expert 5 years, current), PHP (Expert 2 years, last used 2006), Shell (Expert 6 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

Other Trainings

• June 2006, Proteomics Informatics Course at Seattle Proteome Center (S PC), NHLBI Proteomics Center at the Institute for Systems Biology.
  
• September 2010, UC Davis Bioinformatics Short Course 2010, Bioinformatics Core at University of California, Davis.