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Cathy Wu, Ph.D.

Cathy Wu

Unidel Edward G. Jefferson Chair in Engineering and Computer Science
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@udel.edu

[Download NIH Biosketch]

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

  • Director, PhD program in Bioinformatics and Systems Biology, UD, 2012–Present
  • Director, Master of Science (MS) in Bioinformatics & Computational Biology; Professional
    Science Master’s (PSM) in Bioinformatics; and Graduate Certificate in Bioinformatics, UD, 2010–Present
  • Edward G. Jefferson Chair and Director, Center for Bioinformatics & Computational Biology;
    Professor, Department of Computer & Information Sciences and Department of Biological
    Sciences; University of Delaware (UD), 2009–Present
  • Co-Director, Bioinformatics Track, M.S. Degree in Biochemistry and Molecular Biology, GUMC,2008–Present
  • Professor (2001-2008), Adjunct Professor (since 2009), Department of Biochemistry and
    Molecular & Cellular Biology; Member, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center(GUMC), 2001–Present
  • Director of Bioinformatics (1999-2001), Director (since 2001), Protein Information Resource
    (PIR), Georgetown University (since 1999) and University of Delaware (since 2009), 1999–Present
  • 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
  • Postdoctoral Fellow, MSU-DOE Plant Research Laboratory, Michigan State University (Advisor:
    Christopher R. Somerville, Member, National Academy of Sciences),1985–1986

Professional Activities

  • External Advisory Panel, NHLBI Proteomics Program, National Institutes of Health (NIH), 2012–Present
  • Board of Directors, SIG Bioinformatics, Association for Computing Machinery (ACM), 2010–Present
  • Grand Challenge Communities (GCC) Task Force, Office of Cyberinfrastructure (OCI), National
    Science Foundation (NSF), 2009–2010
  • Board on Research Data and Information (BRDI), National Research Council (NRC), 2008–2010
  • Board of Directors; Executive Committee (since 2010), US Human Proteome Organization (US HUPO), 2008–Present
  • Executive Editor, Journal of Proteomics and Bioinformatics, 2008–Present
  • TeraGrid Scientific Advisory Board, National Science Foundation (NSF), 2006–2010
  • Council (2012-2014; 2005-2008), Human Proteome Organization (HUPO), 2005–Present
  • 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 (>50): ACM BCB-2013 (Conference Co–Chair); BioCreative IV, 2012, III (Steering Committee); BIBM-2012 (Conference Co–Chair), BIBM-2009 (Program Committee Co-Chair); USHUPO–2008 (Conference Co–Chair)
  • Over 140 Invited Presentations to universities, companies, and conferences

Grant Awards

  • 1144726, NSF/DGE, IGERT: Systems Biology of Cells in Engineered Environments (SBE2). Role: Co-PI (Jul2012–Jun2017)
  • 2R01GM080646-06 & 3R01GM80646-07S1, 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)
  • DOE/FOA-0000368, Experimental Systems-Biology Approaches for Clostridia-Based Bioenergy Production. Role: Co-PI (Sep2011–Aug2014)
  • 8P20GM103446, NIH/NIGMS, Delaware INBRE Role: Bioinformatics Core Director. (Nov 2009–Feb2014)
  • 1G08 LM010720-01, NIH/NLM, Linking Text Mining and Data Mining for Biomedical Knowledge Discovery. Role: PI (Aug2010–Aug2013)
  • 1U41HG006104-01, NIH/NHGRI, UniProt: A Centralized Protein Sequence and Function Resource. Role: Co-PI (Sep2010–Jul2013)
  • 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)
  • 3R01GM080646-04S2, NIH/NIGMS, Pro: A Protein Ontology in Open Biomedical Ontologies. Role: PI (Sep2009–April2012)

Books

  1. Wu CH and Chen C. (Editors) (2011). Bioinformatics for Comparative Proteomics. Series Methods in Molecular Biology, Volume 694, Series Editor: Walker, John M. 387p. Humana Press. ISBN: 978-1-60761-976-5.
  2. Wang J, Wu CH and Wang P. (Editors) (2003) Computational Biology and Genome Informatics. World Scientific. ISBN 981-238-257-7.
  3. Wu CH and McLarty J. (2000) Neural Networks and Genome Informatics. Methods in Computational Biology and Biochemistry, Volume 1, Series Editor: Konopka, AK. 205 p. Elsevier Science. ISBN 0 08 042800 2.

Journal Special Issues

  1. Arighi CN, Cohen KB, Hirschman L, Lu Z, Tudor OC, Wiegers T, Wilbur J, Wu CH. (Editors) (2014) BioCreative-IV Virtual Issue. Database 2014; bau039 . [doi:10.1093/database/bau039]
  2. Wu CH, Arighi CN, Cohen KB, Hirschman L, Krallinger M, Lu Z, Mattingly C, Valencia A, Wiegers TC, Wilbur WJ. (Editors) (2012) BioCreative-2012 Virtual Issue. Database 2012; bas049 . [doi:10.1093/database/bas049]
  3. Arighi CN, Cohen KB, Hirschman L, Krallinger M, Lu Z, Valencia A, Wilbur J, Wu CH. (Editors) (2011). The Third BioCreative – Critical Assessment of Information Extraction in Biology Challenge. BMC Bioinformatics, Volume 12, Supplement 8.

Refereed Publications (selected from >230 peer-reviewed publications)

Google Scholar (>18,000 citations, h-index: 48, i10-index: 113)
NIH MyBibliography
ResearchGate

  1. Ross KE, Arighi CN, Ren J, Wu CH.(2013) Construction of protein phosphorylation networks by data mining, text mining, and ontology integration: Analysis of the spindle checkpoint. Database 2013; (accepted)
  2. Gonzalez AJ, Liao L, Wu CH. (2013) Prediction of contact matrix for protein-protein interaction. Bioinformatics 2013; Mar 13.
  3. Tudor CO, Arighi CN, Wang Q, Wu CH, Vijay-Shanker K. (2012) The eFIP system for text mining of protein
    interaction networks of phosphorylated proteins    . Database 2012; bas044.
  4. Wang Q, Arighi CN, King BL, Polson SW, Vincent J, Chen C, Huang H, Kingham B, Page ST, Rendino
    MF, Thomas WK, Udwary DW, Wu CH, North East Bioinformatics Collaborative Curation Team. (2012) Community annotation and bioinformatics workforce development in concert – Little skate genome annotation workshops and jamborees. Database 2012, bar064.
  5. Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A, D’Eustachio P, Smith B,
    Blake JA, Wu CH. (2011) The representation of protein complexes in the protein ontology (PRO). BMC Bioinformatics 2011; 12, 371.
  6. Chen C, Natale DA, Finn RD, Huang H, Zhang J, Wu CH, Mazumder R. (2011) Representative Proteomes: a
    stable, scalable and unbiased proteome set for sequence analysis and functional annotation    . PLOS One
    2011; 6(4), e18910.
  7. Huang H, McGarvey PB, Suzek BE, Mazumder R, Zhang J, Chen Y, and Wu CH. (2011) A comprehensive
    protein-centric ID mapping service for molecular data integration    . Bioinformatics 2011; 27, 1190-1191.
  8. Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D’Eustachio P, Evsikov AV,
    Huang H, Nchoutmboube J, Roberts NV, Smith B, Wu CH. (2011) The Protein Ontology (PRO): A structured
    representation of protein forms and complexes    . Nucl. Acids Res. 2011; 39, D539-545. [PMC3013777]
  9. Hu ZZ, Kagan BL, Ariazic EA, Rosenthala DS, Zhanga L, Li JV, Huang H, Wu CH, Jordan VC, Riegela
    AT, Wellsteina A. (2011) Proteomic analysis of pathways involved in estrogen-induced growth and apoptosis in breast cancer cells. PLOS One 2011; 6(6), e20410.
  10. Mazumder R, Natale DA, Julio JA, Yeh LS, Wu CH. (2010) Community annotation in biology. Biology Direct 2010; 5, 12.
  11. McGarvey PB, Huang H, Mazumder R, Zhang J, Chen Y, Zhang C, Cammer S, Will R, Odle M, Sobral B,
    Moore M, Wu CH. (2009) Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets. PLOS One 2009; 4, e7162.
  12. 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.
  13. 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.
  14. 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.
  15. Qui P, Wang ZJ, Liu KR, Hu ZZ, Wu CH. (2007) Dependence network modeling for biomarker identification. Bioinformatics 23, 198-206.
  16. 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]
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. Hirschman L, Park JC, Tsujii J, Wong L, Wu CH. (2002) Accomplishments and challenges in literature data mining for Biology. Bioinformatics 2002; 18: 1553-1561.

Synergistic Activities

  • Bioinformatics Resources – databases and bioinformatics tools to support research and education:
    The Protein Information Resource (proteininformationresource.org) [Wu, Director] and UniProt (www.uniprot.org) [Wu, Co-PI] support genomic, proteomic and systems biology research with over 10 million hits per month from over 100,000 unique sites worldwide.
  • Community Standards and Ontologies – Protein Ontology Consortium [Wu, PI] develops an ontology for proteins in the OBO (Open Biomedical Ontologies) framework (2007–present).
  • Degree Program – (i) Master’s program in Bioinformatics and Computational Biology (MS, PSM and Graduate Certificate) (Fall 2010) [Wu, Director], University of Delaware; (ii) PhD program in Bioinformatics and Systems Biology (Fall 2012) [Wu, Director], University of Delaware; (iii) Bioinformatics Track, MS in Biochemistry and Molecular Biology (Fall 2008) [Wu, Co-Director],Georgetown University.

Collaborators and Other Affiliations

  • UniProt Consortium: Rolf Apweiler & Alex Bateman (European Bioinformatics Institute, UK); Ioannis Xenarios (Swiss Institute of Bioinformatics, Switzerland)
  • Protein Ontology Consortium: Judy Blake & Carol Bult (The Jackson Lab, ME); Barry Smith (SUNY Buffalo, NY); Peter D’Eustachio (NYU, NY)
  • BioCreative Consortium: Lynette Hirschman (MITRE, MA); John Wilbur (NCBI, National Library of Medicine, NIH, MD); Alfonso Valencia (Spanish National Cancer Institute, Spain)

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Center for Bioinformatics and Computational Biology
205 Delaware Biotechnology Institute · 15 Innovation Way · Newark, DE 19711, USA
Phone: 302-831-6173 · Email: bioinformatics@udel.edu