Cathy H. Wu, Ph.D.        

Edward G. Jefferson Chair of Bioinformatics & Computational Biology
Director, Center for Bioinformatics & Computational Biology (CBCB)
Director, Protein Information Resource (PIR)
Professor, Computer & Information Sciences
Professor, Biological Sciences
University of Delaware
15 Innovation Way, Suite 205
Newark, DE  19711-5449
Phone:  302-831-8869   Email:  wuc@dbi.udel.edu

Research Interests

Bioinformatics and Computational Biology: Biological Text Mining, Biological Ontology, Computational Systems Biology, Protein Structure-Function-Network Analysis, Bioinformatics Cyberinfrastructure

[Detailed Research Interests] [Current Projects]

Professional Preparation

BS, Plant Pathology, National Taiwan University, Taiwan, 1978
MS, Plant Pathology, Purdue University, West Lafayette, IN, 1982
PhD, Plant Pathology, Purdue University, West Lafayette, IN, 1984
Postdoc, Molecular Biology, Michigan State University, East Lansing, MI, 1986
MS, Computer Science, University of Texas at Tyler, Tyler, TX, 1989               

Appointments

• Edward G. Jefferson Chair of Bioinformatics & Computational Biology Professor, Computer & Information Sciences and Biological Sciences Director, Center for Bioinformatics & Computational Biology Director, Master's program in Bioinformatics and Computational Biology University of Delaware, January 2009–present
• Director, Protein Information Resource (PIR), 2001–present
• Professor (2001–2008), Adjunct Professor (since 2009), Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, 2001–present
• Director of Bioinformatics, National Biomedical Research Foundation, Georgetown University Medical Center, 1999–2002
• Assistant Professor (1990–1994), Associate Professor (1994–1998), Professor (1998–1999), Department of Epidemiology & Biomathematics, University of Texas Health Center at Tyler, 1990–1999
• Assistant Professor, Department of Mathematics and Computer Science, University of Texas at Tyler, 1989–1994
• Research Scientist, Dept. of Plant Pathology & Microbiology, Texas A&M University, 1986–1987

Professional Activities

• Board on Research Data and Information (BRDI), National Research Council (NRC), 2008–Present
• Board of Directors, US Human Proteome Organization (US HUPO), 2008–Present
• Editorial Board, Journal of Proteomics and Bioinformatics, 2008–Present
• TeraGrid Scientific Advisory Board, National Science Foundation (NSF), 2006–Present
• Council, Human Proteome Organization (HUPO), 2005–2008
• Advisory Board, Protein Data Bank (PDB), 2005–Present
• Advisory Committee, Protein Structure Initiative, National Institute of General Medical Sciences, National Institutes of Health (NIH), 2002–Present
• Board of Directors (2000–2004), Education Committee (since 2003), Member (since 2000), International Society for Computational Biology (ISCB), 2000–Present
• Conference/Workshop Organizing Committee (since 2001): BIBM-2009, -2008; USHUPO-2009, -2008; PAG-2009; ISMB-2008, -2007, -2004, -2002; PSB-2006, -2003, -2002; EITC-2008, -2007, -2004, -2002; CBGI-2002, -2001; BIOKDD-2001; BIBE-2001
• Grant Review/Site Visit (since 2001): NSF-BDI, PGRP, IIS; NIH-CSR, NIGMS, NLM, NCI, NIDA, NCRR; DOE
• Over 100 Invited Presentations to universities, companies, and conferences

Current Grant Awards

• 3R01GM080646-04S2, NIH/NIGMS, Pro: A Protein Ontology in Open Biomedical Ontologies. Role: PI (Sep2009–April2012)
• DBI-0850319, NSF/DBI, Linking Text Mining with Ontology and Systems Biology. Role: PI (Sep2009–Aug2012)
• 1137427, NSF/IIS, III: Small: Women in Bioinformatics Initiative at ACM BCB 2011. Role: Co-PI (Jun2011–May2012)
• 1U41HG006104-01, NIH/NHGRI, UniProt: A Centralized Protein Sequence and Function Resource. Role: Co-PI (Sep2010–Jul2013)
• 1G08 LM010720-01, NIH/NLM, Linking Text Mining and Data Mining for Biomedical Knowledge Discovery. Role: PI (Aug2010–Aug2013)
• 3P20RR016472, NIH/NCRR, Delaware INBRE Role: Bioinformatics Core Director. Role: PI (Nov 2009–Feb2014)
• DOE/FOA-0000368, Experimental Systems-Biology Approaches for Clostridia-Based Bioenergy Production. Role: Co-PI (Sep2011–Aug2014)
• 2R01GM080646-06, NIH/NiGMS, PRO: A Protein Ontology in Open Biomedical Ontologies. Role: PI (Sep2011–Aug2015)
• 1062520, NSF/DBI, ABI Development: Integrative Bioinformatics for Knowledge Discovery of PTM Networks. Role: PI (Jul2011–Jun2015)

Books

1. Wu CH, McLarty J. (2000) Neural Networks and Genome Informatics. Methods in Computational Biology and Biochemistry, Volume 1, Series Editor A. K. Konopka, Elsevier Science.
2. Wang J, Wu CH, Wang P. (Eds) (2003) Computational Biology and Genome Informatics. World Scientific.
3. Wu CH, Chen CM. (Eds) (2010) Bioinformatics for Comparative Proteomics. Humana Press. Methods in Molecular Biology.

Refereed Publications (selected from ~140 peer-reviewed publications)

1. Wu CH, Yeh LS, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu Z, Kourtesis P, Ledley RS, Suzek BE, Vinayaka CR, Zhang J, Barker WC. (2003) The Protein Information Resource. Nucleic Acids Research 31:345-347.
2. Wu CH, Huang H, Nikolskaya A, Hu Z, Barker WC. (2004) The iProClass integrated database for protein functional analysis. Computaional. Biology & Chemistry 28, 87-96.
3. Hu ZZ, Narayanaswamy M, Ravikumar KE, Vijay-Shanker K, Wu CH. (2005) Literature mining and database annotation of protein phosphorylation using a rule-based system. Bioinformatics  21, 2759–2765.
4. Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O’Donovan C, Redaschi N, Suzek B. (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Research 34, D187-191.
5. Petrova NV, Wu CH. (2006) Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. BMC Bioinformatics 7, 312. [Faculty of 1000 Biology]
6. Qui P, Wang ZJ, Liu KR, Hu ZZ, Wu CH. (2007) Dependence network modeling for biomarker identification. Bioinformatics 23, 198-206.
7. Mazumder R, Hu ZZ, Vinayaka CR, Sagripanti J-L, Frost SDW, Pond SLK, Wu CH. (2007) Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines. Virus Genes 35, 175-186.
8. Huang H, Hu ZZ, Arighi C, Wu CH. (2007) Integration of bioinformatics resources for functional analysis of gene expression and proteomic data. Frontiers in Bioscience 12, 5071-5088.
9. Hu ZZ, Huang H, Cheema A, Jung M, Dritschilo A, Wu CH. (2008) Integrated bioinformatics for radiation-induced pathway analysis from proteomics and microarray data. Journal of Proteomics & Bioinformatics 1, 47-60.
10. Arighi CN, Liu H, Natale D, Barker WC, Drabkin HJ, Blake J, Smith B, Wu CH. (2009) TGF-beta signaling proteins and the Protein Ontology. BMC Bioinformatics (in press)

Synergistic Activities

• Bioinformatics Resources – databases and bioinformatics tools to support research and education: The Protein Information Resource (http://proteininformationresource.org/) [Wu, Director] (2001–present).and UniProt Consortium (www.uniprot.org) [Wu, Co-PI] (2002–present) provide international resources on proteins to support genomic, proteomic and systems biology research and are accessible by researchers worldwide with over 10 million hits per month from over 100,000 unique sites. The Resource Center for Biodefense Proteomics Research (www.proteomicsresource.org) [Wu, Co-PI] provides an integrated system for knowledge dissemination from the NIAID Biodefense Proteomics Research program (2004–present).
• Community Standards and Ontologies – Protein Ontology Consortium [Wu, PI] develops an ontology for proteins in the OBO (Open Biomedical Ontologies) framework (2007–present). As part of the caBIG (Cancer Biomedical Informatics Grid), gridPIR [Wu, PI] is a reference application in the caGRID architecture (2005–2007).
• Degree Program – degree and curriculum development for the Bioinformatics Track [Wu, Co-Director], M.S. in Biochemistry & Molecular Biology, Georgetown University, Fall 2009.

Collaborators and Other Affiliations

• UniProt Consortium: Rolf Apweiler (European Bioinformatics Institute, UK); Amos Bairoch (Swiss Institute of Bioinformatics, Switzerland)
• Protein Ontology Consortium: Judy Blake (The Jackson Lab, ME); Barry Smith (SUNY Buffalo, NY)
• BioCreative Consortium: Lynette Hirschman (MITRE, MA); John Wilbur (NCBI, National Library of Medicine, NIH, MD); Alfonso Valencia (Spanish National Cancer Institute, Spain)