Education

Employment

• July 2018 - present Research Associate Professor
  Department of Computer and Information Sciences, Delaware Biotechnology Institute, University of Delaware, Newark DE, USA
• December 2008 - June 2018 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

• 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)

• KSFinder—a knowledge graph model for link prediction of novel phosphorylated substrates of kinases

  Manju Anandakrishnan, Karen E. Ross, Chuming Chen, Vijay Shanker, Julie Cowart, Cathy H. Wu
  PeerJ, 2023, 11:e16164, DOI:https://doi.org/10.7717/peerj.16164

• UniProt: the Universal Protein Knowledgebase in 2023

  UniProt consortium
  Nucleic Acid Research Volume 51, Issue D, https://doi.org/10.1093/nar/gkac1052

• A knowledge graph representation learning approach to predict novel kinase–substrate interactions
  

  Sachin Gavali, Karen Ross, Chuming Chen, Julie Cowart and Cathy H. Wu
  Molecular Omics, 2022, DOI: 10.1039/D1MO00521A

• iPTMnet RESTful API for Post-translational Modification Network Analysis
  

  Sachin Gavali, Karen E. Ross, Julie Cowart, Chuming Chen & Cathy H. Wu
  In: KC, D.B. (eds) Computational Methods for Predicting Post-Translational Modification Sites. Methods in Molecular Biology, vol 2499. Humana, New York, NY. (2022) DOI: https://doi.org/10.1007/978-1-0716-2317-6_10

• COVID-19 knowledge graph from semantic integration of biomedical literature and databases
  

  Chuming Chen, Karen E Ross, Sachin Gavali, Julie E Cowart, Cathy H Wu
  Bioinformatics, btab694, Published: 06 October 2021

• UniProt: the universal protein knowledgebase in 2021

  UniProt consortium
  Nucleic Acid Research Volume 49, Issue D1, 8 January 2021, Pages D480–D489, https://doi.org/10.1093/nar/gkaa1100

• Protein ontology on the semantic web for knowledge discovery

  Chuming Chen, Hongzhan Huang, Karen E. Ross, Julie E. Cowart, Cecilia N. Arighi, Cathy H. Wu & Darren A. Natale
  Scientific Data volume 7, Article number: 337 (2020)

• Understanding ER+ Breast Cancer Dormancy Using Bioinspired Synthetic Matrices for Long‐Term 3D Culture and Insights into Late Recurrence

  Elisa M. Ovadia, Lina Pradhan, Lisa A. Sawicki, Julie E. Cowart, Rebecca E. Huber, Shawn W. Polson, Chuming Chen, Kenneth L. van Golen, Karen E. Ross, Cathy H. Wu, April M. Kloxin
  Advanced Biosystems, First published:30 June 2020 https://doi.org/10.1002/adbi.202000119

• piNET: a versatile web platform for downstream analysis and visualization of proteomics data

  Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Najafabadi, Wen Niu, Chuming Chen,Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dušica Vidović, Jake Jaffe, Michael MacCoss, Cathy Wu, Ajay Pillai, Avi Ma’ayan, Stephan Schürer, Michal Kouril, Mario Medvedovic, Jarek Meller
  Nucleic Acids Research, gkaa436, https://doi.org/10.1093/nar/gkaa436. Published: 29 May 2020

• UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

  Alistair MacDougall, Vladimir Volynkin, Rabie Saidi, Diego Poggioli, Hermann Zellner, Emma Hatton-Ellis, Vishal Joshi, Claire O'Donovan, Sandra Orchard, Andrea H Auchincloss, Delphine Baratin, Jerven Bolleman, Elisabeth Coudert, Edouard de Castro, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Cecilia Arighi, Qinghua Wang, Chuming Chen, Hongzhan Huang, John Garavelli, C R Vinayaka, Lai-Su Yeh, Darren A Natale, Kati Laiho, Maria Martin, UniProt Consortium
  Bioinformatics, btaa485, https://doi.org/10.1093/bioinformatics/btaa485

• RESTful API for iPTMnet: a resource for protein post-translational modification network discovery

  Sachin Gavali, Julie Cowart, Chuming Chen, Karen E Ross, Cecilia Arighi, Cathy H Wu
  Database, Volume 2020, 2020, baz157, https://doi.org/10.1093/database/baz157. Published: 12 May 2020

• FAIR adoption, assessment and challenges at UniProt

  Leyla Garcia, Jerven Bolleman, Sebastien Gehant, Nicole Redaschi, Maria Martin & UniProt Consortium
  Scientific Data, volume 6, Article number: 175 (2019), PMCID: PMC6754384

• Genome sequencing and transcript analysis of Hemileia vastatrix reveal expression dynamics of candidate effectors dependent on host compatibility

  Brenda Neves Porto, Eveline Teixeira Caixeta , Sandra Marisa Mathioni, Pedro Marcus Pereira Vidigal, Laércio Zambolim, Eunize Maciel Zambolim, Nicole Donofrio, Shawn W. Polson, Thiago Andrade Maia, Chuming Chen, Modupe Adetunji, Brewster Kingham, Ronaldo José Durigan Dalio, Mário Lúcio Vilela de Resende
  PLoS One. 2019 Apr 18;14(4):e0215598. doi: 10.1371/journal.pone.0215598. eCollection 2019. PMID: 30998802

• PIRSitePredict for protein functional site prediction using position-specific rules

  Chuming Chen, Qinghua Wang, Hongzhan Huang, Cholanayakanahalli R Vinayaka, John S Garavelli, Cecilia N Arighi, Darren A Natale, Cathy H Wu
  Database, Volume 2019, 1 January 2019, baz026, https://doi.org/10.1093/database/baz026.

• UniProt: a worldwide hub of protein knowledge

  UniProt Consortium
  Nucleic Acides Res. 2018, Nov 5. doi: 10.1093/nar/gky1049.

• Transcriptional profiling of liver during the critical embryo-to-hatchling transition period in the chicken (Gallus gallus)

  Larry A. Cogburn, Nares Trakooljul, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Wilfrid Carré, Xiaofei Wang and Harold B. White III
  BMC Genomics 2018, 19:695. https://doi.org/10.1186/s12864-018-5080-4.

• Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources

  Liang-Chin Huang, Karen E. Ross, Timothy R. Baffi, Harold Drabkin, Krzysztof J. Kochut, Zheng Ruan, Peter D’Eustachio, Daniel McSkimming, Cecilia Arighi, Chuming Chen, Darren A. Natale, Cynthia Smith, Pascale Gaudet, Alexandra C. Newton, Cathy Wu & Natarajan Kannan
  Scientific Reports volume 8, Article number: 6518 (2018) doi:10.1038/s41598-018-24457-1

• Protein Bioinformatics Databases and Resources

  Chuming Chen, Hongzhan Huang, Cathy H. Wu
  Methods in Molecular Biology Voulme: 1558, pp. 3-39. doi: 10.1007/978-1-4939-6783-4_1 published February 02, 2017

• UniProt: the universal protein knowledgebase

  The UniProt Consortium
  Nucl. Acids Res. doi: 10.1093/nar/gkw1099 First published online: November 29, 2016

• Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

  Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH
  Nucleic Acids Res 2016 Nov 28. pii: gkw1075. [Epub ahead of print]

• Computational Clustering for Viral Reference Proteomes

  Chuming Chen, Hongzhan Huang, Raja Mazumder, Darren A. Natale, Peter B. McGarvey, Jian Zhang, Shawn W. Polson, Yuqi Wang, Cathy H. Wu and UniProt Consortium
  Bioinformatics 2016. doi: 10.1093/bioinformatics/btw110

• RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism

  Christopher W. Resnyk, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Jean Simon, Elisabeth Le Bihan-Duval, Michel J. Duclos and Larry A. Cogburn
  PLoS ONE 2015. 10(10): e0139549. doi:10.1371/journal.pone.0139549

• An Integrated Approach for Analyzing Clinical Genomic Variant Data from Next-Generation Sequencing

  Erin L. Crowgey, Deborah L. Stabley, Chuming Chen, Hongzhan Huang, Katherine M. Robbins, Shawn W. Polson, Katia Sol-Church, Cathy H. Wu
  J Biomol Tech. 2015 jbt.15-2601-002. doi: 10.7171/jbt.15-2601-002, PMCID: PMC4310222

• UniProt: a hub for protein information

  The UniProt Consortium
  Nucl. Acids Res. doi: 10.1093/nar/gku989 First published online: October 27, 2014

• SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

  Jennifer Wyffels, Benjamin L. King, James Vincent, Chuming Chen, Cathy H. Wu, Shawn W. Polson
  F1000Research 2014, 3:191 (doi: 10.12688/f1000research.4996.1)

• Software for pre-processing Illumina next-generation sequencing short read sequences

  Chuming Chen, Sari S Khaleel, Hongzhan Huang and Cathy H Wu
  Source Code for Biology and Medicine 2014, 9:8, doi:10.1186/1751-0473-9-8

• Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data

  Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K; UniProt Consortium
  Database (Oxford). 2014 Mar 12;2014:bau016. doi: 10.1093/database/bau016

• Activities at the Universal Protein Resource (UniProt)

  The UniProt Consortium
  Nucl. Acids Res. first published online November 18, 2013 doi:10.1093/nar/gkt1140

• A fast Peptide Match Service for UniProt Knowledgebase

  Chuming Chen, Zhiwen Li, Hongzhan Huang, Baris E. Suzek, Cathy H. Wu, and UniProt Consortium
  Bioinformatics, first published online August 19, 2013 doi:10.1093/bioinformatics/btt484 (2013)

• Elevated FGF21 secretion, PGC-1α and ketogenic enzyme expression are hallmarks of iron-sulfur cluster depletion in human skeletal muscle

  Daniel R. Crooks, Thanemozhi G. Natarajan, Suh Young Jeong, Chuming Chen, Sun Young Park, Hongzhan Huang, Manik C. Ghosh, Wing-Hang Tong, Ronald G. Haller, Cathy Wu, and Tracey A. Rouault
  Hum. Mol. Genet. first published online August 13, 2013 doi:10.1093/hmg/ddt393 (2013)

• Respiratory chain deficiency due to PE-S cluster deficiency in skeletal muscle leads to a systemic starvation response characterized by increased FGF-21 secretion and up-regulation of ketogenic enzyme HMGCS2 in skeletal muscle fibers of ISCU myopthy pati.

  Crooks, Daniel and Natarajan, Thanemozhi and Chen, Chuming and Huang, Hongzhan and Ghosh, Manik and Tong, Wing-Hang and Haller, Ronald and Wu, Cathy and Rouault, Tracey
  American Journal of Hematology, vol. 88, no. 5. pp. E45-E45. (2013)

• 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: Lectures, Live Demos and Exercises

• 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-BIBM-2017 (IEEE International Conference on Bioinformatics and Bioengineering 2017)
• Program committee of IEEE-BIBM-2016 (IEEE International Conference on Bioinformatics and Bioengineering 2016)
• Program committee of IEEE-BIBM-2015 (IEEE International Conference on Bioinformatics and Bioengineering 2015)
• Program committee of IEEE-BIBM-2014 (IEEE International Conference on Bioinformatics and Bioengineering 2014)
• Program committee of IEEE-BIBM-2013 (IEEE International Conference on Bioinformatics and Bioengineering 2013)
• Program committee of IEEE-BIBM-2012 (IEEE International Conference on Bioinformatics and Bioengineering 2012)
• Program committee of IEEE-BIBM-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

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.