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An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities.

Sathiamurthy M, Peters B, Bui HH, Sidney J, Mokili J, Wilson SS, Fleri W, McGuinness DL, Bourne PE, Sette A.

Immunome Res. 2005 Sep 20;1(1):2.PMID: 16305755 [PubMed]Related articlesFree article

EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB).

Beaver JE, Bourne PE, Ponomarenko JV.

Immunome Res. 2007 Feb 21;3:3.PMID: 17313688 [PubMed]Related articlesFree article

The immune epitope database 2.0.

Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B.

Nucleic Acids Res. 2010 Jan;38(Database issue):D854-62. Epub 2009 Nov 11.PMID: 19906713 [PubMed - indexed for MEDLINE]Related articlesFree article

An analysis of the epitope knowledge related to Mycobacteria.

Blythe MJ, Zhang Q, Vaughan K, de Castro R Jr, Salimi N, Bui HH, Lewinsohn DM, Ernst JD, Peters B, Sette A.

Immunome Res. 2007 Dec 14;3:10.PMID: 18081934 [PubMed - in process]Related articlesFree article

Meeting Report: NIH Workshop on the Tuberculosis Immune Epitope Database.

Ernst JD, Lewinsohn DM, Behar S, Blythe M, Schlesinger LS, Kornfeld H, Sette A.

Tuberculosis (Edinb). 2008 Jul;88(4):366-70. Epub 2007 Dec 18.PMID: 18068490 [PubMed - indexed for MEDLINE]Related articlesFree article

A roadmap for the immunomics of category A-C pathogens.

Sette A, Fleri W, Peters B, Sathiamurthy M, Bui HH, Wilson S.

Immunity. 2005 Feb;22(2):155-61.PMID: 15773067 [PubMed - indexed for MEDLINE]Related articles

The design and implementation of the immune epitope database and analysis resource.

Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger SP, Stewart S, Surko P, Way S, Wilson S, Sette A.

Immunogenetics. 2005 Jun;57(5):326-36. Epub 2005 May 14.PMID: 15895191 [PubMed - indexed for MEDLINE]Related articles

Ab and T cell epitopes of influenza A virus, knowledge and opportunities.

Bui HH, Peters B, Assarsson E, Mbawuike I, Sette A.

Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):246-51.PMID: 17200302 [PubMed - indexed for MEDLINE]Related articlesFree article

Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines.

Bui HH, Sidney J, Li W, Fusseder N, Sette A.

BMC Bioinformatics. 2007 Sep 26;8:361.PMID: 17897458 [PubMed - indexed for MEDLINE]Related articlesFree article

Curation of complex, context-dependent immunological data.

Vita R, Vaughan K, Zarebski L, Salimi N, Fleri W, Grey H, Sathiamurthy M, Mokili J, Bui HH, Bourne PE, Ponomarenko J, de Castro R Jr, Chan RK, Sidney J, Wilson SS, Stewart S, Way S, Peters B, Sette A.

BMC Bioinformatics. 2006 Jul 12;7:341.PMID: 16836764 [PubMed - indexed for MEDLINE]Related articlesFree article

Immune epitope database analysis resource (IEDB-AR).

Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W513-8. Epub 2008 May 31.PMID: 18515843 [PubMed - indexed for MEDLINE]Related articlesFree article

A new asset for pathogen informatics--the Enteropathogen Resource Integration Center (ERIC), an NIAID Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Disease.

Greene JM, Plunkett G 3rd, Burland V, Glasner J, Cabot E, Anderson B, Neeno-Eckwall E, Qiu Y, Mau B, Rusch M, Liss P, Hampton T, Pot D, Shaker M, Shaull L, Shetty P, Shi C, Whitmore J, Wong M, Zaremba S, Blattner FR, Perna NT.

Adv Exp Med Biol. 2007;603:28-42.PMID: 17966403 [PubMed - indexed for MEDLINE]Related articles

Classification of the universe of immune epitope literature: representation and knowledge gaps.

Davies V, Vaughan K, Damle R, Peters B, Sette A.

PLoS One. 2009 Sep 14;4(9):e6948.PMID: 19774228 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of epitope information related to Bacillus anthracis and Clostridium botulinum.

Zarebski LM, Vaughan K, Sidney J, Peters B, Grey H, Janda KD, Casadevall A, Sette A.

Expert Rev Vaccines. 2008 Feb;7(1):55-74. Review.PMID: 18251694 [PubMed - indexed for MEDLINE]Related articles

The MGED Ontology: A Framework for Describing Functional Genomics Experiments.

Stoeckert CJ, Parkinson H.

Comp Funct Genomics. 2003;4(1):127-32.PMID: 18629093 [PubMed - in process]Related articlesFree article

Antibody-protein interactions: benchmark datasets and prediction tools evaluation.

Ponomarenko JV, Bourne PE.

BMC Struct Biol. 2007 Oct 2;7:64.PMID: 17910770 [PubMed - indexed for MEDLINE]Related articlesFree article

CED: a conformational epitope database.

Huang J, Honda W.

BMC Immunol. 2006 Apr 7;7:7.PMID: 16603068 [PubMed - indexed for MEDLINE]Related articlesFree article

BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence.

Squires B, Macken C, Garcia-Sastre A, Godbole S, Noronha J, Hunt V, Chang R, Larsen CN, Klem E, Biersack K, Scheuermann RH.

Nucleic Acids Res. 2008 Jan;36(Database issue):D497-503. Epub 2007 Oct 26.PMID: 17965094 [PubMed - indexed for MEDLINE]Related articlesFree article

Integrating epitope data into the emerging web of biomedical knowledge resources.

Peters B, Sette A.

Nat Rev Immunol. 2007 Jun;7(6):485-90. Review.PMID: 17479127 [PubMed - indexed for MEDLINE]Related articles

The Innate Immune Database (IIDB).

Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H.

BMC Immunol. 2008 Mar 5;9:7.PMID: 18321385 [PubMed - indexed for MEDLINE]Related articlesFree article