Abbas AK, Lichtman A: Cellular and Molecular Immunology. 2005, Saunders, 5

Google Scholar

Nobrega A, Grandien A, Haury M, Hecker L, Malanchère E, Coutinho A: Functional diversity and clonal frequencies of reactivity in the available antibody repertoire. European Journal of Immunology. 1998, 28 (4): 1204-1215. 10.1002/(SICI)1521-4141(199804)28:04<1204::AID-IMMU1204>3.0.CO;2-G.

Article
CAS
PubMed
Google Scholar

Quintana FJJ, Merbl Y, Sahar E, Domany E, Cohen IR: Antigen-chip technology for accessing global information about the state of the body. Lupus. 2006, 15 (7): 428-430. 10.1191/0961203306lu2328oa.

Article
CAS
PubMed
Google Scholar

Nobrega A, Haury M, Grandien A, Malanchère E, Sundblad A, Coutinho A: Global analysis of antibody repertoires. II. Evidence for specificity, self-selection and the immunological "homunculus" of antibodies in normal serum. European Journal of Immunology. 1993, 23 (11): 2851-2859. 10.1002/eji.1830231119.

Article
CAS
PubMed
Google Scholar

Haury M, Grandien A, Sundblad A, Coutinho A, Nobrega A: Global analysis of antibody repertoires. 1. An immunoblot method for the quantitative screening of a large number of reactivities. Scandinavian Journal of Immunology. 1994, 39: 79-87. 10.1111/j.1365-3083.1994.tb03343.x.

Article
CAS
PubMed
Google Scholar

Robinson WH, DiGennaro C, Hueber W, Haab BB, Kamachi M, Dean EJ, Fournel S, Fong D, Genovese MC, de Vegvar HEN, Skriner K, Hirschberg DL, Morris RI, Muller S, Pruijn GJ, van Venrooij WJ, Smolen JS, Brown PO, Steinman L, Utz PJ: Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat Med. 2002, 8 (3): 295-301. 10.1038/nm0302-295.

Article
CAS
PubMed
Google Scholar

Quintana FJ: Functional immunomics: Microarray analysis of IgG autoantibody repertoires predicts the future response of mice to induced diabetes. Proceedings of the National Academy of Sciences. 2004, 101 (suppl_2): 14615-14621.

Article
CAS
Google Scholar

Merbl Y, Itzchak R, Vider-Shalit T, Louzoun Y, Quintana FJ, Vadai E, Eisenbach L, Cohen IR: A systems immunology approach to the host-tumor interaction: large-scale patterns of natural autoantibodies distinguish healthy and tumor-bearing mice. PloS One. 2009, 4 (6): e6053-10.1371/journal.pone.0006053.

Article
PubMed Central
PubMed
Google Scholar

Cekaite L, Haug O, Myklebost O, Aldrin M, Østenstad B, Holden M, Frigessi A, Hovig E, Sioud M: Analysis of the humoral immune response to immunoselected phage-displayed peptides by a microarray-based method. PROTEOMICS. 2004, 4 (9): 2572-2582. 10.1002/pmic.200300768.

Article
CAS
PubMed
Google Scholar

Bongartz J, Bruni N, Or-Guil M: Epitope mapping using randomly generated peptide libraries. Methods in Molecular Biology (Clifton, N.J.). 2009, 524: 237-246. 10.1007/978-1-59745-450-6_17.

Article
CAS
Google Scholar

Legutki JB, Magee DM, Stafford P, Johnston SA: A general method for characterization of humoral immunity induced by a vaccine or infection. Vaccine. 2010, 28 (28): 4529-4537. 10.1016/j.vaccine.2010.04.061.

Article
CAS
PubMed
Google Scholar

Reddy MM, Wilson R, Wilson J, Connell S, Gocke A, Hynan L, German D, Kodadek T: Identification of Candidate IgG Biomarkers for Alzheimer's Disease via Combinatorial Library Screening. Cell. 2011, 144: 132-142. 10.1016/j.cell.2010.11.054.

Article
PubMed Central
CAS
PubMed
Google Scholar

Weiser AA, Or-Guil M, Tapia V, Leichsenring A, Schuchhardt J, Frömmel C, Volkmer-Engert R: SPOT synthesis: Reliability of array-based measurement of peptide binding affinity. Analytical Biochemistry. 2005, 342 (2): 300-311. 10.1016/j.ab.2005.04.033.

Article
CAS
PubMed
Google Scholar

Tapia V, Bongartz J, Schutkowski M, Bruni N, Weiser A, Ay B, Volkmer R, Or-Guil M: Affinity profiling using the peptide microarray technology: A case study. Analytical Biochemistry. 2007, 363: 108-118. 10.1016/j.ab.2006.12.043.

Article
CAS
PubMed
Google Scholar

Brown JR, Stafford P, Johnston SA, Dinu V: Statistical methods for analyzing immunosignatures. BMC Bioinformatics. 2011, 12: 349-10.1186/1471-2105-12-349.

Article
PubMed Central
PubMed
Google Scholar

Chou PY, Fasman GD: Prediction of the secondary structure of proteins from their amino acid sequence. Advances in Enzymology and Related Areas of Molecular Biology. 1978, 47: 45-148.

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 (19): 5425-5432. 10.1021/bi00367a013.

Article
CAS
PubMed
Google Scholar

Emini EA, Hughes JV, Perlow DS, Boger J: Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. Journal of Virology. 1985, 55 (3): 836-839.

PubMed Central
CAS
PubMed
Google Scholar

Hopp TP, Woods KR: Prediction of protein antigenic determinants from amino acid sequences. Proceedings of the National Academy of Sciences of the USA. 1981, 78 (6): 3824-3828. 10.1073/pnas.78.6.3824.

Article
PubMed Central
CAS
PubMed
Google Scholar

Mandrika I, Prusis P, Yahorava S, Tars K, Wikberg JE: QSAR of multiple mutated antibodies. Journal of Molecular Recognition. 2007, 20 (2): 97-102. 10.1002/jmr.817.

Article
CAS
PubMed
Google Scholar

Mandrika I, Prusis P, Yahorava S, Shikhagaie M, Wikberg JE: Proteochemometric modelling of antibody-antigen interactions using SPOT synthesised peptide arrays. Protein Engineering, Design and Selection. 2007, gzm022-

Google Scholar

Mandrika I, Prusis P, Bergström J, Yahorava S, Wikberg JES: Improving the affinity of antigens for mutated antibodies by use of statistical molecular design. Journal of Peptide Science: An Official Publication of the European Peptide Society. 2008, 14 (7): 786-796.

Article
CAS
Google Scholar

De Boer RJ, Perelson AS: T Cell Repertoires and Competitive Exclusion. Journal of Theoretical Biology. 1994, 169 (4): 375-390. 10.1006/jtbi.1994.1160.

Article
CAS
PubMed
Google Scholar

Perelson AS: Immune Network Theory. Immunological Reviews. 1989, 110: 5-36. 10.1111/j.1600-065X.1989.tb00025.x.

Article
CAS
PubMed
Google Scholar

Sulzer B, Perelson AS: Equilibrium binding of multivalent ligands to cells: Effects of cell and receptor density. Mathematical Biosciences. 1996, 135 (2): 147-185. 10.1016/0025-5564(96)00022-3.

Article
CAS
PubMed
Google Scholar

Perelson AS, Weisbuch G: Immunology for physicists. Reviews of Modern Physics. 1997, 69 (4): 1219-10.1103/RevModPhys.69.1219.

Article
CAS
Google Scholar

Alkhamis KA, Wurster DE: Prediction of adsorption from multicomponent solutions by activated carbon using single-solute parameters. Part II-Proposed equation. AAPS PharmSciTech. 2002, 3 (3): E23-10.1208/pt030323.

Article
PubMed
Google Scholar

Rausch S, Huehn J, Kirchhoff D, Rzepecka J, Schnoeller C, Pillai S, Loddenkemper C, Scheffold A, Hamann A, Lucius R, Hartmann S: Functional Analysis of Effector and Regulatory T Cells in a Parasitic Nematode Infection. Infect Immun. 2008, 76 (5): 1908-1919. 10.1128/IAI.01233-07.

Article
PubMed Central
CAS
PubMed
Google Scholar

Sandberg M, Eriksson L, Jonsson J, Sjöström M, Wold S: New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids. Journal of Medicinal Chemistry. 1998, 41 (14): 2481-2491. 10.1021/jm9700575.

Article
CAS
PubMed
Google Scholar

Kolaskar A, Tongaonkar PC: A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Letters. 1990, 276 (1-2): 172-174. 10.1016/0014-5793(90)80535-Q.

Article
CAS
PubMed
Google Scholar

Berek C, Griffiths GM, Milstein C: Molecular events during maturation of the immune response to oxazolone. Nature. 1985, 316 (6027): 412-418. 10.1038/316412a0.

Article
CAS
PubMed
Google Scholar

Brissac C, Nobrega A, Carneiro J, Stewart J: Functional diversity of natural IgM. Int Immunol. 1999, 11 (9): 1501-1507. 10.1093/intimm/11.9.1501.

Article
CAS
PubMed
Google Scholar

Jerne NK: The natural-selection theory of antibody formation. Proceedings of the National Academy of Sciences of the USA. 1955, 41 (11): 849-10.1073/pnas.41.11.849.

Article
PubMed Central
CAS
PubMed
Google Scholar

Perelson AS, Oster GF: Theoretical studies of clonal selection: Minimal antibody repertoire size and reliability of self-non-self discrimination. Journal of Theoretical Biology. 1979, 81 (4): 645-670. 10.1016/0022-5193(79)90275-3.

Article
CAS
PubMed
Google Scholar

Janeway C, Shlomchik MJ, Walport : Immunobiology. 2004, Garland Science, 6

Google Scholar

McCoy KD, Stoel M, Stettler R, Merky P, Fink K, Senn BM, Schaer C, Massacand J, Odermatt B, Oettgen HC, Zinkernagel RM, Bos NA, Hengartner H, Macpherson AJ, Harris NL: Polyclonal and Specific Antibodies Mediate Protective Immunity against Enteric Helminth Infection. Cell Host & Microbe. 2008, 4 (4): 362-373. 10.1016/j.chom.2008.08.014.

Article
CAS
Google Scholar

Greenbaum JA, Andersen PH, Blythe M, Bui H, Cachau RE, Crowe J, Davies M, Kolaskar AS, Lund O, Morrison S, Mumey B, Ofran Y, Pellequer J, Pinilla C, Ponomarenko JV, Raghava GPS, van Regenmortel MHV, 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. Journal of Molecular Recognition. 2007, 20 (2): 75-82. 10.1002/jmr.815.

Article
CAS
PubMed
Google Scholar

EL-Manzalawy Y, Honavar V: Recent advances in B-cell epitope prediction methods. Immunome Research. 2010, 6 (Suppl 2): S2-10.1186/1745-7580-6-S2-S2.

Article
PubMed Central
PubMed
Google Scholar

Blythe MJ, Flower DR: Benchmarking B cell epitope prediction: Underperformance of existing methods. Protein Science: A Publication of the Protein Society. 2005, 14: 246-248.

Article
CAS
Google Scholar

Mahrenholz CC, Tapia V, Stigler RD, Volkmer R: A study to assess the cross-reactivity of cellulose membrane-bound peptides with detection systems: an analysis at the amino acid level. Journal of Peptide Science: An Official Publication of the European Peptide Society. 2010, 16 (6): 297-302.

CAS
Google Scholar

Weinstein JA, Jiang N, White RA, Fisher DS, Quake SR: High-Throughput Sequencing of the Zebrafish Antibody Repertoire. Science. 2009, 324 (5928): 807-810. 10.1126/science.1170020.

Article
PubMed Central
CAS
PubMed
Google Scholar

Tiller T, Tsuiji M, Yurasov S, Velinzon K, Nussenzweig MC, Wardemann H: Autoreactivity in human IgG+ memory B cells. Immunity. 2007, 26 (2): 205-213. 10.1016/j.immuni.2007.01.009.

Article
PubMed Central
CAS
PubMed
Google Scholar

Meffre E, Schaefer A, Wardemann H, Wilson P, Davis E, Nussenzweig MC: Surrogate Light Chain Expressing Human Peripheral B Cells Produce Self-reactive Antibodies. The Journal of Experimental Medicine. 2004, 199: 145-150.

Article
PubMed Central
CAS
PubMed
Google Scholar

Wardemann H, Yurasov S, Schaefer A, Young JW, Meffre E, Nussenzweig MC: Predominant autoantibody production by early human B cell precursors. Science (New York, N.Y.). 2003, 301 (5638): 1374-1377. 10.1126/science.1086907.

Article
CAS
Google Scholar

Tiller T, Meffre E, Yurasov S, Tsuiji M, Nussenzweig MC, Wardemann H: Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning. Journal of immunological methods. 2008, 329 (1-2): 112-124. 10.1016/j.jim.2007.09.017.

Article
PubMed Central
CAS
PubMed
Google Scholar

Haury M, Sundblad A, Grandien A, Barreau C, Coutinho A, Nobrega A: The repertoire of serum IgM in normal mice is largely independent of external antigenic contact. European journal of immunology. 1997, 27 (6): 1557-1563. 10.1002/eji.1830270635.

Article
CAS
PubMed
Google Scholar

Rosenwald S, Kafri R, Lancet D: Test of a Statistical Model for Molecular Recognition in Biological Repertoires. Journal of Theoretical Biology. 2002, 216 (3): 327-336. 10.1006/jtbi.2002.2538.

Article
CAS
PubMed
Google Scholar

Horovitz A, Rigbi M: Protein-protein interactions: Additivity of the free energies of association of amino acid residues. Journal of Theoretical Biology. 1985, 116: 149-159. 10.1016/S0022-5193(85)80135-1.

Article
CAS
PubMed
Google Scholar

Free SM, Wilson JW: A Mathematical Contribution to Structure-Activity Studies. Journal of Medicinal Chemistry. 1964, 7 (4): 395-399. 10.1021/jm00334a001.

Article
CAS
PubMed
Google Scholar

Mevik B, Wehrens R: The pls Package: Principal Component and Partial Least Squares Regression in R. Journal of Statistical Software. 2007, 18 (2): 1-24.

Article
Google Scholar

Team RDC: R: A Language and Environment for Statistical Computing. 2009, Vienna, Austria

Google Scholar

Stacklies W, Redestig H, Scholz M, Walther D, Selbig J: pcaMethods a bioconductor package providing PCA methods for incomplete data. Bioinformatics. 2007, 23 (9): 1164-1167. 10.1093/bioinformatics/btm069.

Article
CAS
PubMed
Google Scholar

Behnke J, Harris PD: Heligmosomoides bakeri: a new name for an old worm?. Trends in Parasitology. 2010

Google Scholar