Cathy H Wu

Summary

Affiliation: Georgetown University
Country: USA

Publications

  1. pmc Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach
    Rajaram Gana
    Department of Biostatistics and Bioinformatics, Georgetown University Medical Center, Washington, DC 20007, USA
    BMC Struct Biol 13:6. 2013
  2. pmc DynGO: a tool for visualizing and mining of Gene Ontology and its associations
    Hongfang Liu
    Department of Information Systems, University of Maryland, Baltimore County, 1000 Hilltop Circle, MD 21050, USA
    BMC Bioinformatics 6:201. 2005
  3. ncbi request reprint The iProClass integrated database for protein functional analysis
    Cathy H Wu
    Georgetown University Medical Center, Washington, DC 20057 1455, USA
    Comput Biol Chem 28:87-96. 2004
  4. ncbi request reprint Protein family classification and functional annotation
    Cathy H Wu
    Georgetown University Medical Center and National Biomedical Research Foundation, 3900 Reservoir Road, NW, Box 571455, Washington, DC 20057 1455, USA
    Comput Biol Chem 27:37-47. 2003
  5. pmc PIRSF: family classification system at the Protein Information Resource
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057 1414, USA
    Nucleic Acids Res 32:D112-4. 2004
  6. pmc Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets
    Peter B McGarvey
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America
    PLoS ONE 4:e7162. 2009
  7. pmc Framework for a protein ontology
    Darren A Natale
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven St, NW, Washington, DC 20007, USA
    BMC Bioinformatics 8:S1. 2007
  8. pmc The Protein Information Resource
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057 1414, USA
    Nucleic Acids Res 31:345-7. 2003
  9. ncbi request reprint Integration of bioinformatics resources for functional analysis of gene expression and proteomic data
    Hongzhan Huang
    Protein Information Resource PIR, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Front Biosci 12:5071-88. 2007
  10. pmc The Universal Protein Resource (UniProt): an expanding universe of protein information
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Washington, DC 20057 1414, USA
    Nucleic Acids Res 34:D187-91. 2006

Research Grants

Detail Information

Publications36

  1. pmc Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach
    Rajaram Gana
    Department of Biostatistics and Bioinformatics, Georgetown University Medical Center, Washington, DC 20007, USA
    BMC Struct Biol 13:6. 2013
    ..Results of applying our approach to S-adenosyl-L-methionine (SAM) binding proteins are presented...
  2. pmc DynGO: a tool for visualizing and mining of Gene Ontology and its associations
    Hongfang Liu
    Department of Information Systems, University of Maryland, Baltimore County, 1000 Hilltop Circle, MD 21050, USA
    BMC Bioinformatics 6:201. 2005
    ..e., genes and gene products annotated with GO terms). Tools that allow users to directly search and inspect relations among all GO terms and their associated genes and gene products from multiple databases are needed...
  3. ncbi request reprint The iProClass integrated database for protein functional analysis
    Cathy H Wu
    Georgetown University Medical Center, Washington, DC 20057 1455, USA
    Comput Biol Chem 28:87-96. 2004
    ..Such studies may serve as a basis for further analysis of protein functional evolution, and its relationship to the co-evolution of metabolic pathways, cellular networks, and organisms...
  4. ncbi request reprint Protein family classification and functional annotation
    Cathy H Wu
    Georgetown University Medical Center and National Biomedical Research Foundation, 3900 Reservoir Road, NW, Box 571455, Washington, DC 20057 1455, USA
    Comput Biol Chem 27:37-47. 2003
    ..It also illustrates that data integration in PIR supports exploration of protein relationships and may reveal protein functional associations beyond sequence homology...
  5. pmc PIRSF: family classification system at the Protein Information Resource
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057 1414, USA
    Nucleic Acids Res 32:D112-4. 2004
    ..PIRSF can be utilized to analyze phylogenetic profiles, to reveal functional convergence and divergence, and to identify interesting relationships between homeomorphic families, domains and structural classes...
  6. pmc Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets
    Peter B McGarvey
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, United States of America
    PLoS ONE 4:e7162. 2009
    ....
  7. pmc Framework for a protein ontology
    Darren A Natale
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, 3300 Whitehaven St, NW, Washington, DC 20007, USA
    BMC Bioinformatics 8:S1. 2007
    ..Here we describe the initial development of PRO, illustrated using human and mouse proteins involved in the transforming growth factor-beta and bone morphogenetic protein signaling pathways...
  8. pmc The Protein Information Resource
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057 1414, USA
    Nucleic Acids Res 31:345-7. 2003
    ..The FTP site provides free download for PSD and NREF biweekly releases and auxiliary databases and files...
  9. ncbi request reprint Integration of bioinformatics resources for functional analysis of gene expression and proteomic data
    Hongzhan Huang
    Protein Information Resource PIR, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Front Biosci 12:5071-88. 2007
    ....
  10. pmc The Universal Protein Resource (UniProt): an expanding universe of protein information
    Cathy H Wu
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Washington, DC 20057 1414, USA
    Nucleic Acids Res 34:D187-91. 2006
    ..A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/...
  11. pmc iProClass: an integrated database of protein family, function and structure information
    Hongzhan Huang
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, 3900 Reservoir Road, NW, Box 571414, Washington, DC 20057 1414, USA
    Nucleic Acids Res 31:390-2. 2003
    ..The data integration in iProClass supports exploration of protein relationships. Such knowledge is fundamental to the understanding of protein evolution, structure and function and crucial to functional genomic and proteomic research...
  12. doi request reprint Protein-centric data integration for functional analysis of comparative proteomics data
    Peter B McGarvey
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
    Methods Mol Biol 694:323-39. 2011
    ..We illustrate with examples how this can aid in identifying important processes from large complex lists...
  13. ncbi request reprint UniRef: comprehensive and non-redundant UniProt reference clusters
    Baris E Suzek
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Bioinformatics 23:1282-8. 2007
    ..Clustering of protein sequence space based on sequence similarity helps organize all sequences into manageable datasets and reduces sampling bias and overrepresentation of sequences...
  14. pmc A comparison study on algorithms of detecting long forms for short forms in biomedical text
    Manabu Torii
    Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, 4000 Resevoir Rd, NW, Washington, DC 20057, USA
    BMC Bioinformatics 8:S5. 2007
    ....
  15. doi request reprint Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebase
    Sona Vasudevan
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
    Methods Mol Biol 694:91-105. 2011
    ..The strict criteria used in this process have rendered high-confidence annotation suitable for UniProtKB/Swiss-Prot features...
  16. ncbi request reprint iProLINK: an integrated protein resource for literature mining
    Zhang Zhi Hu
    Georgetown University Medical Center, 3900 Reservoir Road, NW, Washington, DC 20057, USA
    Comput Biol Chem 28:409-16. 2004
    ..iProLINK is freely accessible at http://pir.georgetown.edu/iprolink, with hypertext links for all downloadable files...
  17. pmc Computational identification of strain-, species- and genus-specific proteins
    Raja Mazumder
    Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057 1414, USA
    BMC Bioinformatics 6:279. 2005
    ..Strain-, species- and genus-specific proteins can provide insight into the criteria that define an organism and its relationship with close relatives. Such proteins can also serve as taxon-specific diagnostic targets...
  18. pmc Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties
    Natalia V Petrova
    Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    BMC Bioinformatics 7:312. 2006
    ....
  19. doi request reprint Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromes
    Winona C Barker
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Virus Genes 39:1-9. 2009
    ..These findings should help predicting the disease potential of emerging and re-emerging flaviviruses and understanding the relationship between protein structure and disease outcome...
  20. pmc BioTagger-GM: a gene/protein name recognition system
    Manabu Torii
    The Imaging Science and Information Systems Center, Department of Oncology, Georgetown University Medical Center, 2115 Wisconsin Avenue NW, Washington, DC 20057, USA
    J Am Med Inform Assoc 16:247-55. 2009
    ..Our goal is to develop a gene/protein name recognition system BioTagger-GM that exploits rich information in terminology sources using powerful machine learning frameworks and system combination...
  21. doi request reprint Protein Ontology: a controlled structured network of protein entities
    Darren A Natale
    Protein Information Resource, Georgetown University Medical Center, WA 20007, USA, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Bioinformatics and Computational Biology, The Jackson Laboratory, Bar Harbor, ME 04609, USA, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, NY 10016, USA, Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA, Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA, Department of Immunology, Duke University Medical Center, Durham, NC 27705, USA and Department of Oral Diagnostic Sciences, University at Buffalo School of Dental Medicine, Buffalo, NY 14214, USA
    Nucleic Acids Res 42:D415-21. 2014
    ..The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. ..
  22. ncbi request reprint Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines
    Raja Mazumder
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Virus Genes 35:175-86. 2007
    ....
  23. pmc Omics-based molecular target and biomarker identification
    Zhang Zhi Hu
    Lombardi Cancer Center, Georgetown University, Washington, DC, USA
    Methods Mol Biol 719:547-71. 2011
    ..We describe a downstream workflow and procedures for functional analysis that focus on biological pathways, from which molecular targets can be derived and proposed for experimental validation...
  24. pmc Community annotation in biology
    Raja Mazumder
    Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
    Biol Direct 5:12. 2010
    ..Based on this study we propose community annotation projects should devote resources to direct solicitation for input and streamlining of the processes or interfaces used to collect this input...
  25. pmc The Protein Ontology: a structured representation of protein forms and complexes
    Darren A Natale
    Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA
    Nucleic Acids Res 39:D539-45. 2011
    ..PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontology Foundry...
  26. pmc A fast Peptide Match service for UniProt Knowledgebase
    Chuming Chen
    Center for Bioinformatics and Computational Biology and Protein Information Resource, University of Delaware, Newark, DE 19711, USA, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneva 4, Switzerland
    Bioinformatics 29:2808-9. 2013
    ..In addition to the web interface, we also provide RESTful web services. The underlying data are updated every 4 weeks in accordance with the UniProt releases...
  27. pmc The Protein Information Resource: an integrated public resource of functional annotation of proteins
    Cathy H Wu
    National Biomedical Research Foundation, Georgetown University Medical Center, 3900 Reservoir Road, NW, Washington, DC 20007, USA
    Nucleic Acids Res 30:35-7. 2002
    ..The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases)...
  28. pmc New developments in the InterPro database
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute Hinxton, Cambridge, UK
    Nucleic Acids Res 35:D224-8. 2007
    ..ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html...
  29. ncbi request reprint Accomplishments and challenges in literature data mining for biology
    Lynette Hirschman
    The MITRE Corporation, USA
    Bioinformatics 18:1553-61. 2002
    ..To encourage participation and accelerate progress in this expanding field, we propose creating challenge evaluations, and we describe two specific applications in this context...
  30. pmc UniProt: the Universal Protein knowledgebase
    Rolf Apweiler
    The EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 32:D115-9. 2004
    ..The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt...
  31. ncbi request reprint Protein sequence databases
    Rolf Apweiler
    The EMBL Outstation The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Curr Opin Chem Biol 8:76-80. 2004
    ..Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium...
  32. pmc The Universal Protein Resource (UniProt)
    Amos Bairoch
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
    Nucleic Acids Res 33:D154-9. 2005
    ..The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks...
  33. pmc InterPro, progress and status in 2005
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 33:D201-5. 2005
    ..The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)...
  34. pmc Plant protein annotation in the UniProt Knowledgebase
    Michel Schneider
    Swiss Institute of Bioinformatics, Centre Medical Universitaire, University of Geneva, 1211 Geneva 4, Switzerland
    Plant Physiol 138:59-66. 2005
    ....
  35. ncbi request reprint Substring selection for biomedical document classification
    Bo Han
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    Bioinformatics 22:2136-42. 2006
    ..92-0.97] when using the proposed attribute selection than when using attributes obtained by the Porter stemmer algorithm (AUC in 0.86-0.93 range). The proposed approach is particularly useful when labeled datasets are small...
  36. ncbi request reprint Dependence network modeling for biomarker identification
    Peng Qiu
    Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, USA
    Bioinformatics 23:198-206. 2007
    ....

Research Grants2

  1. PRO: A Protein Ontology in Open Biomedical Ontologies
    Cathy Wu; Fiscal Year: 2007
    ..The PRO ontology will allow researchers to explore functional and evolutionary relationships of proteins to improve understanding of disease and identify potential diagnostic and therapeutic targets. ..