Chuming Chen, Ph.D. ()
Research Assistant Professor
Department of Computer and Information Sciences
Center for Bioinformatics and Computational Biology
Protein Information Resource
Delaware Biotechnology Institute
University of Delaware
15 Innovation Way, Suite 205
Newark, DE 19711
Email: chenc At udel DoT edu
Homepage: http://www.cis.udel.edu/~chenc
Tel: +1(302)831-3426(O)
Fax: +1(302)831-4841
PIR Home: http://ProteinInformationResource.org
UniProt Home: http://www.uniprot.org

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

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 Research Topics:
Next-generation Sequencing data analysis, Genomics, URA automated mass annotation of proteins, Mass Spectra Proteomics Informatics, Semantic Web, Description Logics, Ontology Engineering, Temporal Database, Network Security, High Performance Computing, Bioinformatics, Data Integration

Past Research Topics:
Non-destructive Integrity Evaluation in Micro-piles, Petroleum Geology, Structural Geology, Geophysics

Current Projects

  • 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

  • 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.

  • 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)


Teaching Experience

May 22-23, 2012
CBCB Bioinformatics Short Course: RNA-Seq Data Analysis
May 23, 2011
NECC Third Skate Genome Annotation Workshop
June 2008 - July 2008
Department of Computer Science and Engineering, University of South Carolina, Columbia SC, USA
August 2002 - December 2002
Department of Computer Science and Engineering, University of South Carolina, Columbia SC, USA
July 2002 - August 2002
Department of Computer Science and Engineering, University of South Carolina, Columbia SC, USA
  • Instructor: CSCE102 (General Applications Programming)

August 2001 - June 2002
Department of Computer Science and Engineering, University of South Carolina, Columbia SC, USA

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


Reviewer

See my Publons profile

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