Publications Relevant to the IEDB

 
 

General IEDB
  • Vita R, Overton JA, Greenbaum JA, Sette A; OBI consortium, Peters B. "Query enhancement through the practical application of ontology: the IEDB and OBI". J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S6. doi: 10.1186/2041-1480-4-S1-S6. Epub 2013 Apr 15. PubMed PMID: 23734660; PubMed Central PMCID: PMC3633001.
  • Salimi N, Fleri W, Peters B, Sette A. "The Immune Epitope Database: A Historical Retrospective of the First Decade". Immunology. 2012 Jun 8. doi:10.1111/j.1365-2567.2012.03611.x. [Epub ahead of print]. PMID: 22681406
  • Ponomarenko J, Papangelopoulos N, Zajonc DM, Peters B, Sette A, Bourne PE. "IEDB-3D: structural data within the immune epitope database". Nucleic Acids Res. 2010 Oct 28. PMID: 21030437
  • Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ Jr, Turner JA, Zheng J; OBI consortium. "Modeling biomedical experimental processes with OBI". J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S7. PMID: 20626927
  • Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. "Hematopoietic cell types: Prototype for a revised cell ontology". J Biomed Inform. 2010 Feb 1. PMID: 20123131
  • Salimi N, Fleri W, Peters B, Sette A. "Design and utilization of epitope-based databases and predictive tools". Immunogenetics. 2010 Apr;62(4):185-96. Epub 2010 Mar 6. PMID: 20213141
  • Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B. "The Immune Epitope Database 2.0". Nucleic Acids Res. 2010 Jan;38(Database issue):D854-62. Epub 2009 Nov 11 PubMed. PMID: 19906713
  • Peters B, Sette A. "Integrating epitope data into the emerging web of biomedical knowledge resources". Nat Rev Immunol. 2007 Jun;7(6):485-90. PMID: 17479127
  • Sette A, Peters B. "Immune epitope mapping in the post-genomic era: lessons for vaccine development". Curr Opin Immunol. 2007 Feb;19(1):106-10. PMID: 17113275
  • Muthuraman Sathiamurthy, Bjoern Peters, Huynh-Hoa Bui, John Sidney, John Mokili, Stephen S Wilson, Ward Fleri, Deborah L McGuinness, Philip E Bourne, and Alessandro Sette. "An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities". Immunome Res. 2005 Sep 20;1(1):2. PMID: 16305755
  • Sette A, Bui, HH, Sidney J, Bourne P, Buus S, Fleri W, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Stewart S, Way S, Wilson SS, Peters B.
    "The Immune Epitope Database and Analysis Resource". Pattern Recognition in Bioinformatics: International Workshop, PRIB 2006, Hong Kong, China, August 20, 2006 : Proceedings, Springer, Jagath C. Rajapakse, Limsoon Wong, Raj Acharya (Eds).
    ISBN: 3540374469 9783540374466
  • 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 S, Stewart S, Surko P, Way S, Wilson S, Sette A. "The Design and Implementation of the Immune Epitope Data Base and Analysis Resource". Immunogenetics. 2005 Jun;57(5):326-36. Epub 2005 May 14. PMID: 15895191
  • 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 S, Stewart S, Surko P, Way S, Wilson S, Sette A. "The Immune Epitope Database and Analysis Resource: from Vision to Blueprint". PLoS Biol. 2005 Mar;3(3):e91. PMID: 15760272
  • Sette A, Fleri W, Peters B, Sathiamurthy M, Bui HH, Wilson S. "A Roadmap for the Immunomics of Category A-C Pathogens". Immunity, 2005 Feb;22(2):155-61. PMID: 15773067
  • Sette A. "The immune epitope database and analysis resource: from vision to blueprint". Genome Inform Ser Workshop Genome Inform. 2004;15(2):299. PMID: 16312048
Epitope Meta-Analyses
  • Kim Y, Yewdell JW, Sette A, Peters B. "Positional bias of MHC class I restricted T-cell epitopes in viral antigens is likely due to a bias in conservation". PLoS Comput Biol. 2013 Jan;9(1):e1002884. doi: 10.1371/journal.pcbi.1002884. Epub 2013 Jan 24. PubMed PMID: 23357871; PubMed Central PMCID: PMC3554532
  • Vaughan K, Kim Y, Sette A. "A comparison of epitope repertoires associated with myasthenia gravis in humans and nonhuman hosts". Autoimmune Dis. 2012;2012:403915. doi: 10.1155/2012/403915. Epub 2012 Dec 2. PMID: 23243503; PubMed Central PMCID: PMC3518085
  • Vaughan K, Peters B, Larche M, Pomes A, Broide D, Sette A. "Strategies to Query and Display Allergy-Derived Epitope Data from the Immune Epitope Database". Int Arch Allergy Immunol. 2012 Nov 21;160(4):334-345. [Epub ahead of print]. PMID: 23172234
  • Kim Y, Vaughan K, Greenbaum J, Peters B, Law M, Sette A. "A Meta-Analysis of the Existing Knowledge of Immunoreactivity against Hepatitis C Virus (HCV)". PLoS One. 2012;7(5):e38028. Epub 2012 May 31. PMID: 22675428; PubMed Central PMCID: PMC3364976
  • Vaughan K, Greenbaum J, Kim Y, Vita R, Chung J, Peters B, Broide D, Goodman R, Grey H, Sette A. "Towards defining molecular determinants recognized by adaptive immunity in allergic disease: an inventory of the available data". J Allergy (Cairo). 2010;2010:628026. Epub 2011 Feb 13. PMID: 21403821
  • Vaughan K, Greenbaum J, Blythe M, Peters B, Sette A. "Meta-analysis of all immune epitope data in the Flavivirus genus: inventory of current immune epitope data status in the context of virus immunity and immunopathology". Viral Immunol. 2010 Jun;23(3):259-84. PMID: 20565291
  • Greenbaum JA, Kotturi MF, Kim Y, Oseroff C, Vaughan K, Salimi N, Vita R, Ponomarenko J, Scheuermann RH, Sette A, Peters B. "Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population". Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20365-70. Epub 2009 Nov 16. PubMed. PMID: 19918065; PubMed Central PMCID: PMC2777968
  • Davies V, Vaughan K, Damle R, Peters B, Sette A. "Classification of the universe of immune epitope literature: representation and knowledge gaps". PLoS One. 2009 Sep 14;4(9):e6948. PubMed. PMID: 19774228
  • Vaughan K, Blythe M, Greenbaum J, Zhang Q, Peters B, Doolan DL, Sette A, "Meta-analysis of immune epitope data for all Plasmodia: overview and applications for malarial immunobiology and vaccine-related issues". Parasite Immunol. 2009 Feb;31(2):78-97. PMID: 19149776
  • Zarebski LM, Vaughan K, Sidney J, Peters B, Grey H, Janda KD, Casadevall A, Sette A. "Analysis of epitope information related to Bacillus anthracis and Clostridium botulinum". Expert Rev Vaccines.
    2008 Feb;7(1):55-74. PMID: 18251694
  • Blythe MJ, Zhang Q, Vaughan K, de Castro R Jr, Salimi N, Bui HH, Lewinsohn DM, Ernst JD, Peters B, Sette A. "An analysis of the epitope knowledge related to Mycobacteria". Immunome Res.
    2007 Dec 14;3(1):10. PMID: 18081934
  • Ernst JD, Lewinsohn DM, Behar S, Blythe M, Schlesinger LS, Kornfeld H, Sette A. "Meeting Report: NIH Workshop on the Tuberculosis Immune Epitope Database". Tuberculosis (Edinb). 2007 Dec 6.
    PMID: 18068490
  • Bui HH, Peters B, Assarsson E, Mbawuike I, Sette A. "Ab and T cell epitopes of influenza A virus, knowledge and opportunities". Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):246-51. PMID: 17200302
Analysis Resource
  • Karosiene E, Rasmussen M, Blicher T, Lund O, Buus S, Nielsen M. "NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ". Immunogenetics.
    2013 Oct;65(10):711-24. doi: 10.1007/s00251-013-0720-y. Epub 2013 Jul 31. PubMed PMID: 23900783
  • Kringelum JV, Nielsen M, Padkjær SB, Lund O. "Structural analysis of B-cell epitopes in antibody:protein complexes". Mol Immunol. 2013 Jan;53(1-2):24-34. doi: 10.1016/j.molimm.2012.06.001. Epub 2012 Jul 10. PMID: 22784991; PubMed Central PMCID: PMC3461403
  • Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B. "Immune epitope database analysis resource". Nucleic Acids Res. 2012 Jul;40 (Web Server issue):W525-30. Epub 2012 May 18. PMID: 22610854
  • Wang P, Sidney J, Kim Y, Sette A, Lund O, Nielsen M, Peters B. "Peptide binding predictions for HLA DR, DP and DQ molecules". BMC Bioinformatics. 2010 Nov 22;11:568. PMID: 21092157; PubMed Central PMCID: PMC2998531
  • Kim Y, Sette A, Peters B. "Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource." J Immunol Methods. 2010 Oct 31. PMID: 21047510
  • Nielsen M, Lund O, Buus S, Lundegaard C. "MHC class II epitope predictive algorithms". Immunology. 2010 Jul;130(3):319-28. Epub 2010 Apr 12. Review. PMID: 20408898
  • Zhang H, Wang P, Papangelopoulos N, Xu Y, Sette A, Bourne PE, Lund O, Ponomarenko J, Nielsen M, Peters B. "Limitations of Ab initio predictions of peptide binding to MHC class II molecules". PLoS One. 2010 Feb 17;5(2):e9272. PubMed PMID: 20174654
  • Kim Y, Sidney J, Pinilla C, Sette A, Peters B. "Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior". BMC Bioinformatics. 2009 Nov 30;10:394. PubMed. PMID: 19948066
  • Zhang H, Lund O, Nielsen M. "The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: Application to MHC-peptide binding". Bioinformatics. 2009 Mar 17. PMID: 19297351
  • Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, Buus S, Nielsen M. "NetMHCpan, a method for MHC class I binding prediction beyond humans". Immunogenetics. 2009 Jan;61(1):1-13. PMID: 19002680
  • Ponomarenko J, H. H. Bui, W. Li, N. Fusseder, P. E. Bourne, A. Sette, B. Peters. (2008). "ElliPro: a new structure-based tool for the prediction of antibody epitopes". BMC Bioinformatics, 9(514). PMID: 19055730
  • Ponomarenko J. V., M. H. C. van Regenmortel (2008) "B-cell epitope prediction". Structural Bioinformatics, Ed: Bourne PE, Gu J. Wiley-Liss; 2nd edition.
  • Lundegaard C., K. Lamberth, M. Harndahl, S. Buus, O. Lund, M. Nielsen. (2008). "NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11". Nucleic Acids Res. 2008 36:W509-12. PMID: 18996943
  • Rapin N., I. Hoof, O. Lund, M. Nielsen. (2008). "MHC motif viewer". Immunogenetics. 60(12): 759-65. PMID: 18766337
  • Nielsen M, Lundegaard C, Blicher T, Peters B, Sette A, Justesen S, Buus S, Lund O. "Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan". PLoS Comput Biol. 2008 Jul 4;4(7):e1000107. PMID: 18604266
  • 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. "Immune epitope database analysis resource (IEDB-AR)". Nucleic Acids Res. 2008 May 31. PMID: 18515843
  • Wang P, Sidney J, Dow C, Mothé B, Sette A, Peters B. "A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach". PLoS Comput Biol.
    2008 Apr 4;4(4):e1000048. PMID: 18389056
  • Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M. "Modeling the adaptive immune system: predictions and simulations". Bioinformatics. 2007 Dec 15;23(24):3265-75. PMID: 18045832
  • Ponomarenko JV, Bourne PE. "Antibody-protein interactions: benchmark datasets and prediction tools evaluation". BMC Struct Biol. 2007 Oct 2;7(1):64. PMID: 17910770
  • Bui HH, Sidney J, Li W, Fusseder N, Sette A. "Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines". BMC Bioinformatics. 2007 Sep 26;8(1):361. PMID: 17897458
  • Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, R�der G, Peters B, Sette A, Lund O, Buus S. "NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence". PLoS ONE. 2007 Aug 29;2(8):e796. PMID: 17726526
  • Greenbaum JA, Andersen PH, Blythe M, Bui HH, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, Mumey B, Ofran Y, Pellequer JL, Pinilla C, Ponomarenko JV, Raghava GP, van Regenmortel MH, Roggen EL, Sette A, Schlessinger A, Sollner J, Zand M, Peters B. "Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools". J Mol Recognit.
    2007 Mar-Apr;20(2):75-82. PMID: 17205610
  • Beaver JE, Bourne PE, Ponomarenko JV. "EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB)". Immunome Res. 2007 Feb 21;3:3. PMID: 17313688
  • Peters B, Bui HH, Frankild S, Nielson M, Lundegaard C, Kostem E, Basch D, Lamberth K, Harndahl M, Fleri W, Wilson SS, Sidney J, Lund O, Buus S, Sette A. "A community resource benchmarking predictions of peptide binding to MHC-I molecules". PLoS Comput Biol. 2006 Jun 9;2(6):e65. Epub 2006 Jun 9. PMID: 16789818
  • Bui HH, Sidney J, Dinh K, Southwood S, Newman MJ, Sette A. "Predicting population coverage of T-cell epitope-based diagnostics and vaccines". BMC Bioinformatics. 2006 Mar 17;7(1):153. PMID: 16545123
  • Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothé BR, Chisari FV, Watkins DI, Sette A. "Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications". Immunogenetics. 2005 Jun;57(5):304-14. Epub 2005 May 3. PMID: 15868141
  • Bjoern Peters and Alessandro Sette. "Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method". BMC Bioinformatics 2005, 6:132.
    PMID: 15927070
Curation
  • Seymour E, Damle R, Sette A, Peters B. "Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation". BMC Bioinformatics. 2011 Dec 19;12:482. PMID: 22182279; PubMed Central PMCID: PMC3314711
  • Vita R, Peters B, Josephs Z, de Matos P, Ennis M, Turner S, Steinbeck C, Seymour E, Zarebski L, Sette A. (2011). "A Model for Collaborative Curation, The IEDB and ChEBI Curation of Non-peptidic Epitopes". Immunome Res. 2011 Apr 1;7(1):1-8. PMID: 21897450
  • Vita R, Peters B, Sette A. "The Curation Guidelines of the Immune Epitope Database and Analysis Resource". Cytometry A. 2008 Aug 7. PMID: 18688821
  • Wang P, Morgan AA, Zhang Q, Sette A, Peters B. "Automating document classification for the Immune Epitope Database". BMC Bioinformatics. 2007 Jul 26;8:269. PMID: 17655769
  • Salimi N, Vita R. "The biocurator: connecting and enhancing scientific data". PLoS Comput Biol. 2006 Oct 27;2(10):e125. No abstract available. PMID: 17069454
  • 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.
    "Curation of complex, context-dependent immunological data". BMC Bioinformatics. 2006 Jul 12;7:341. PMID: 16836764