Research Topics
| Cathy H WuSummaryAffiliation: Georgetown University Country: USA Publications
Research Grants
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Detail Information
Publications
DynGO: a tool for visualizing and mining of Gene Ontology and its associationsHongfang 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...
The iProClass integrated database for protein functional analysisCathy 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...- Protein family classification and functional annotationCathy 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... - PIRSF: family classification system at the Protein Information ResourceCathy 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... - Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targetsPeter 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.... - Framework for a protein ontologyDarren 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... - The Protein Information ResourceCathy 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... - Integration of bioinformatics resources for functional analysis of gene expression and proteomic dataHongzhan 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.... - A comparison study on algorithms of detecting long forms for short forms in biomedical textManabu Torii
Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, 4000 Resevoir Rd, NW, Washington, DC 20057, USA
BMC Bioinformatics 8:S5. 2007.... - iProClass: an integrated database of protein family, function and structure informationHongzhan 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... 
Protein-centric data integration for functional analysis of comparative proteomics dataPeter 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...- The Universal Protein Resource (UniProt): an expanding universe of protein informationCathy 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/... - Structure-guided rule-based annotation of protein functional sites in UniProt knowledgebaseSona 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... - iProLINK: an integrated protein resource for literature miningZhang-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... - Computational identification of strain-, species- and genus-specific proteinsRaja 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... - Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural propertiesNatalia 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.... - Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccinesRaja Mazumder
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
Virus Genes 35:175-86. 2007.... - BioTagger-GM: a gene/protein name recognition systemManabu 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... - Sequence signatures in envelope protein may determine whether flaviviruses produce hemorrhagic or encephalitic syndromesWinona 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... - UniRef: comprehensive and non-redundant UniProt reference clustersBaris 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... - Omics-based molecular target and biomarker identificationZhang 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... - Community annotation in biologyRaja Mazumder
Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC 20007, USA
Biol Direct 5:12. 2010..REVIEWERS: This article was reviewed by I. King Jordan, Daniel Haft and Yuriy Gusev... - The Protein Information Resource: an integrated public resource of functional annotation of proteinsCathy 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)... - The Protein Ontology: a structured representation of protein forms and complexesDarren 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... - Accomplishments and challenges in literature data mining for biologyLynette 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... - UniProt: the Universal Protein knowledgebaseRolf 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... - Protein sequence databasesRolf 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... - 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... - InterPro, progress and status in 2005Nicola 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)... - Plant protein annotation in the UniProt KnowledgebaseMichel Schneider
Swiss Institute of Bioinformatics, Centre Medical Universitaire, University of Geneva, 1211 Geneva 4, Switzerland
Plant Physiol 138:59-66. 2005.... - Substring selection for biomedical document classificationBo 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... - New developments in the InterPro databaseNicola 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... - Dependence network modeling for biomarker identificationPeng Qiu
Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, USA
Bioinformatics 23:198-206. 2007....
Research Grants
- PRO: A Protein Ontology in Open Biomedical OntologiesCathy 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. ..