McFarland BJ, Beeson C: **Binding interactions between peptides and proteins of the class II major histocompatibility complex.**
*Med Res Rev* 2002, **22:**168–203.

Article
CAS
PubMed
Google Scholar

Yaneva R, Schneeweiss C, Zacharias M, Springer S: **Peptide binding to MHC class I and II proteins: new avenues from new methods.**
*Mol Immunol* 2010, **47:**649–657.

Article
CAS
PubMed
Google Scholar

Benacerraf B: **A hypothesis to relate the specificity of T lymphocytes and the activity of I region-specific Ir genes in macrophages and B lymphocytes.**
*J Immunol* 1978, **120:**1809–1812.

CAS
PubMed
Google Scholar

Rosenthal AS, Barcinski MA, Blake JT: **Determinant selection is a macrophage dependent immune response gene function.**
*Nature* 1977, **267:**156–158.

Article
CAS
PubMed
Google Scholar

Schaeffer EB, Sette A, Johnson DL, Bekoff MC, Smith JA, Grey HM, Buus S: **Relative contribution of "determinant selection" and "holes in the T-cell repertoire" to T-cell responses.**
*Proc Natl Acad Sci USA* 1989, **86:**4649–4653.

Article
CAS
PubMed
Google Scholar

Lanzavecchia A: **Antigen-specific interaction between T and B cells.**
*Nature* 1985, **314:**537–539.

Article
CAS
PubMed
Google Scholar

Sette A, Moutaftsi M, Moyron-Quiroz J, McCausland MM, Davies DH, Johnston RJ, Peters B, Rafii-El-Idrissi BM, Hoffmann J, Su HP, Singh K, Garboczi DN, Head S, Grey H, Felgner PL, Crotty S: **Selective CD4+ T cell help for antibody responses to a large viral pathogen: deterministic linkage of specificities.**
*Immunity* 2008, **28:**847–858.

Article
CAS
PubMed
Google Scholar

Mason D: **A very high level of crossreactivity is an essential feature of the T-cell receptor.**
*Immunol Today* 1998, **19:**395–404.

Article
CAS
PubMed
Google Scholar

Wucherpfennig KW, Allen PM, Celada F, Cohen IR, De BR, Garcia KC, Goldstein B, Greenspan R, Hafler D, Hodgkin P, Huseby ES, Krakauer DC, Nemazee D, Perelson AS, Pinilla C, Strong RK, Sercarz EE: **Polyspecificity of T cell and B cell receptor recognition.**
*Semin Immunol* 2007, **19:**216–224.

Article
CAS
PubMed
Google Scholar

Munz C: **Antigen processing via autophagy--not only for MHC class II presentation anymore?**
*Curr Opin Immunol* 2010, **22:**89–93.

Article
PubMed
Google Scholar

Moutaftsi M, Tscharke DC, Vaughan K, Koelle DM, Stern L, Calvo-Calle M, Ennis F, Terajima M, Sutter G, Crotty S, Drexler I, Franchini G, Yewdell JW, Head SR, Blum J, Peters B, Sette A: **Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens.**
*Future Microbiol* 2010, **5:**221–239.

Article
CAS
PubMed
Google Scholar

Harada M, Matsueda S, Yao A, Noguchi M, Itoh K: **Vaccination of cytotoxic T lymphocyte-directed peptides elicited and spread humoral and Th1-type immune responses to prostate-specific antigen protein in a prostate cancer patient.**
*J Immunother* 2005, **28:**368–375.

Article
CAS
PubMed
Google Scholar

Corman JM, Sercarz EE, Nanda NK: **Recognition of prostate-specific antigenic peptide determinants by human CD4 and CD8 T cells.**
*Clin Exp Immunol* 1998, **114:**166–172.

Article
CAS
PubMed
Google Scholar

Van Regenmortel MH: **What is a B-cell epitope?**
*Methods Mol Biol* 2009, **524:**3–20.

Article
CAS
PubMed
Google Scholar

Batista FD, Iber D, Neuberger MS: **B cells acquire antigen from target cells after synapse formation.**
*Nature* 2001, **411:**489–494.

Article
CAS
PubMed
Google Scholar

Bekeredjian-Ding I, Inamura S, Giese T, Moll H, Endres S, Sing A, Zahringer U, Hartmann G: **Staphylococcus aureus protein A triggers T cell-independent B cell proliferation by sensitizing B cells for TLR2 ligands.**
*J Immunol* 2007, **178:**2803–2812.

CAS
PubMed
Google Scholar

Rappuoli R: **Bridging the knowledge gaps in vaccine design.**
*Nat Biotechnol* 2007, **25:**1361–1366.

Article
CAS
PubMed
Google Scholar

Agarwal A, Nayak BP, Rao KV: **B cell responses to a peptide epitope. VII. Antigen-dependent modulation of the germinal center reaction.**
*J Immunol* 1998, **161:**5832–5841.

CAS
PubMed
Google Scholar

Agarwal A, Rao KV: **B cell responses to a peptide epitope: III. Differential T helper cell thresholds in recruitment of B cell fine specificities.**
*J Immunol* 1997, **159:**1077–1085.

CAS
PubMed
Google Scholar

De Groot AS: **Immunomics: discovering new targets for vaccines and therapeutics.**
*Drug Discov Today* 2006, **11:**203–209.

Article
CAS
PubMed
Google Scholar

Pizza M, Scarlato V, Masignani V, Giuliani MM, Arico B, Comanducci M, Jennings GT, Baldi L, Bartolini E, Capecchi B, Galeotti CL, Luzzi E, Manetti R, Marchetti E, Mora M, Nuti S, Ratti G, Santini L, Savino S, Scarselli M, Storni E, Zuo P, Broeker M, Hundt E, Knapp B, Blair E, Mason T, Tettelin H, Hood DW, Jeffries AC, Saunders NJ, Granoff DM, Venter JC, Moxon ER, Grandi G, Rappuoli R: **Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing.**
*Science* 2000, **287:**1816–1820.

Article
CAS
PubMed
Google Scholar

Robson NC, Hoves S, Maraskovsky E, Schnurr M: **Presentation of tumour antigens by dendritic cells and challenges faced.**
*Curr Opin Immunol* 2010, **22:**137–144.

Article
CAS
PubMed
Google Scholar

Van der Bruggen P, Van den Eynde BJ: **Processing and presentation of tumor antigens and vaccination strategies.**
*Curr Opin Immunol* 2006, **18:**98–104.

Article
CAS
PubMed
Google Scholar

Hopp TP, Woods KR: **Prediction of protein antigenic determinants from amino acid sequences.**
*Proc Natl Acad Sci USA* 1981, **78:**3824–3828.

Article
CAS
PubMed
Google Scholar

Parker JM, Guo D, Hodges RS: **New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites.**
*Biochemistry* 1986, **25:**5425–5432.

Article
CAS
PubMed
Google Scholar

Blythe MJ, Flower DR: **Benchmarking B cell epitope prediction: underperformance of existing methods.**
*Protein Sci* 2005, **14:**246–248.

Article
CAS
PubMed
Google Scholar

Davydov YI, Tonevitsky AG: **Prediction of linear B-cell epitopes.**
*Molecular Biology* 2009, **43:**150–153.

Article
CAS
Google Scholar

Larsen JE, Lund O, Nielsen M: **Improved method for predicting linear B-cell epitopes.**
*Immunome Res* 2006, **2:**2.

Article
PubMed
Google Scholar

Bremel RD, Homan EJ: **An integrated approach to epitope analysis I: Dimensional reduction, visualization and prediction of MHC binding using amino acid principal components and regression approaches.**
*Immunome Res* 2010.,**6**(1)**:**

Hopp TP: **Use of hydrophilicity plotting procedures to identify protein antigenic segments and other interaction sites.**
*Methods Enzymol* 1989, **178:**571–585.

Article
CAS
PubMed
Google Scholar

De Groot AS, Berzofsky JA: **From genome to vaccine--new immunoinformatics tools for vaccine design.**
*Methods* 2004, **34:**425–428.

Article
CAS
PubMed
Google Scholar

Doytchinova IA, Flower DR: **QSAR and the Prediction of T-Cell Epitopes.**
*Curr Proteomics* 2008, **5:**73–95.

Article
CAS
Google Scholar

Lafuente EM, Reche PA: **Prediction of MHC-peptide binding: a systematic and comprehensive overview.**
*Curr Pharm Des* 2009, **15:**3209–3220.

Article
CAS
PubMed
Google Scholar

Tian F, Lv F, Zhou P, Yang Q, Jalbout AF: **Toward prediction of binding affinities between the MHC protein and its peptide ligands using quantitative structure-affinity relationship approach.**
*Protein Pept Lett* 2008, **15:**1033–1043.

Article
CAS
PubMed
Google Scholar

Davies MN, Flower DR: **Static energy analysis of MHC class I and class II peptide-binding affinity.**
*Methods Mol Biol* 2007, **409:**309–320.

Article
CAS
PubMed
Google Scholar

Zhao C, Zhang H, Luan F, Zhang R, Liu M, Hu Z, Fan B: **QSAR method for prediction of protein-peptide binding affinity: application to MHC class I molecule HLA-A*0201.**
*J Mol Graph Model* 2007, **26:**246–254.

Article
CAS
PubMed
Google Scholar

Toseland CP, Clayton DJ, McSparron H, Hemsley SL, Blythe MJ, Paine K, Doytchinova IA, Guan P, Hattotuwagama CK, Flower DR: **AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data.**
*Immunome Res* 2005, **1:**4.

Article
PubMed
Google Scholar

Blythe MJ, Doytchinova IA, Flower DR: **JenPep: a database of quantitative functional peptide data for immunology.**
*Bioinformatics* 2002, **18:**434–439.

Article
CAS
PubMed
Google Scholar

McSparron H, Blythe MJ, Zygouri C, Doytchinova IA, Flower DR: **JenPep: a novel computational information resource for immunobiology and vaccinology.**
*J Chem Inf Comput Sci* 2003, **43:**1276–1287.

CAS
PubMed
Google Scholar

Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, Bui HH, Grey H, Sette A: **A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus.**
*Nat Biotechnol* 2006, **24:**817–819.

Article
CAS
PubMed
Google Scholar

Moutaftsi M, Bui HH, Peters B, Sidney J, Salek-Ardakani S, Oseroff C, Pasquetto V, Crotty S, Croft M, Lefkowitz EJ, Grey H, Sette A: **Vaccinia virus-specific CD4+ T cell responses target a set of antigens largely distinct from those targeted by CD8+ T cell responses.**
*J Immunol* 2007, **178:**6814–6820.

CAS
PubMed
Google Scholar

Kennedy R, Poland GA: **T-Cell epitope discovery for variola and vaccinia viruses.**
*Rev Med Virol* 2007, **17:**93–113.

Article
CAS
PubMed
Google Scholar

Cruciani G, Baroni M, Carosati E, Clementi M, Valigi R, Clementi S: **Peptide studies by means of principal properties of amino acids derived from MIF descriptors.**
*Journal of Chemometrics* 2004, **18:**146–155.

Article
CAS
Google Scholar

Eriksson L, Johansson E, Kettaneh-Wold N, Trygg J, Wikstrom C, Wold S: *Multi and Megavariate Data Analysis. Part I: Basic Principles and Applications*. 2nd edition. Umetrics Academy, Umea, Sweden; 2006.

Google Scholar

Kall L, Krogh A, Sonnhammer EL: **A combined transmembrane topology and signal peptide prediction method.**
*J Mol Biol* 2004, **338:**1027–1036.

Article
CAS
PubMed
Google Scholar

Reynolds SM, Kall L, Riffle ME, Bilmes JA, Noble WS: **Transmembrane topology and signal peptide prediction using dynamic bayesian networks.**
*PLoS Comput Biol* 2008, **4:**e1000213.

Article
PubMed
Google Scholar

Jones DT: **Improving the accuracy of transmembrane protein topology prediction using evolutionary information.**
*Bioinformatics* 2007, **23:**538–544.

Article
CAS
PubMed
Google Scholar

Krogh A, Larsson B, von HG, Sonnhammer EL: **Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.**
*J Mol Biol* 2001, **305:**567–580.

Article
CAS
PubMed
Google Scholar

Savitzky A, Golay MJE: **Smoothing and differentiation of data by simplified least squares procedures.**
*Anal Chem* 1964, **36:**1627–1639.

Article
CAS
Google Scholar

Kuklin NA, Clark DJ, Secore S, Cook J, Cope LD, McNeely T, Noble L, Brown MJ, Zorman JK, Wang XM, Pancari G, Fan H, Isett K, Burgess B, Bryan J, Brownlow M, George H, Meinz M, Liddell ME, Kelly R, Schultz L, Montgomery D, Onishi J, Losada M, Martin M, Ebert T, Tan CY, Schofield TL, Nagy E, Meineke A, Joyce JG, Kurtz MB, Caulfield MJ, Jansen KU, McClements W, Anderson AS: **A novel Staphylococcus aureus vaccine: iron surface determinant B induces rapid antibody responses in rhesus macaques and specific increased survival in a murine S. aureus sepsis model.**
*Infect Immun* 2006, **74:**2215–2223.

Article
CAS
PubMed
Google Scholar

Brown M, Kowalski R, Zorman J, Wang XM, Towne V, Zhao Q, Secore S, Finnefrock AC, Ebert T, Pancari G, Isett K, Zhang Y, Anderson AS, Montgomery D, Cope L, McNeely T: **Selection and characterization of murine monoclonal antibodies to Staphylococcus aureus iron-regulated surface determinant B with functional activity in vitro and in vivo.**
*Clin Vaccine Immunol* 2009, **16:**1095–1104.

Article
CAS
PubMed
Google Scholar

Burnie JP, Matthews RC, Carter T, Beaulieu E, Donohoe M, Chapman C, Williamson P, Hodgetts SJ: **Identification of an immunodominant ABC transporter in methicillin-resistant Staphylococcus aureus infections.**
*Infect Immun* 2000, **68:**3200–3209.

Article
CAS
PubMed
Google Scholar

Gardy JL, Spencer C, Wang K, Ester M, Tusnady GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, Brinkman FS: **PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria.**
*Nucleic Acids Res* 2003, **31:**3613–3617.

Article
CAS
PubMed
Google Scholar

Kotturi MF, Assarsson E, Peters B, Grey H, Oseroff C, Pasquetto V, Sette A: **Of mice and humans: how good are HLA transgenic mice as a model of human immune responses?**
*Immunome Res* 2009, **5:**3.

Article
PubMed
Google Scholar

Pasquetto V, Bui HH, Giannino R, Banh C, Mirza F, Sidney J, Oseroff C, Tscharke DC, Irvine K, Bennink JR, Peters B, Southwood S, Cerundolo V, Grey H, Yewdell JW, Sette A: **HLA-A*0201, HLA-A*1101, and HLA-B*0702 transgenic mice recognize numerous poxvirus determinants from a wide variety of viral gene products.**
*J Immunol* 2005, **175:**5504–5515.

CAS
PubMed
Google Scholar

De Groot AS, Martin W: **Reducing risk, improving outcomes: bioengineering less immunogenic protein therapeutics.**
*Clin Immunol* 2009, **131:**189–201.

Article
CAS
PubMed
Google Scholar

Bergtold A, Desai DD, Gavhane A, Clynes R: **Cell surface recycling of internalized antigen permits dendritic cell priming of B cells.**
*Immunity* 2005, **23:**503–514.

Article
CAS
PubMed
Google Scholar

Wykes M, Pombo A, Jenkins C, MacPherson GG: **Dendritic cells interact directly with naive B lymphocytes to transfer antigen and initiate class switching in a primary T-dependent response.**
*J Immunol* 1998, **161:**1313–1319.

CAS
PubMed
Google Scholar

Delamarre L, Pack M, Chang H, Mellman I, Trombetta ES: **Differential lysosomal proteolysis in antigen-presenting cells determines antigen fate.**
*Science* 2005, **307:**1630–1634.

Article
CAS
PubMed
Google Scholar

Yewdell JW, Del VM: **Immunodominance in TCD8+ responses to viruses: cell biology, cellular immunology, and mathematical models.**
*Immunity* 2004, **21:**149–153.

Article
CAS
PubMed
Google Scholar

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, **31:**78–97.

Article
CAS
PubMed
Google Scholar