318
Views
45
CrossRef citations to date
0
Altmetric
Review

Immunoinformatics and its relevance to understanding human immune disease

&
Pages 145-157 | Published online: 10 Jan 2014

References

  • Ehreth J. The global value of vaccination. Vaccine 21, 596–600 (2003).
  • Brusic V, August JT. The changing field of vaccine development in the genomics era. Pharmacogenomics 5(6), 597–600 (2004).
  • Knudsen TB, Kledal TN, Andersen O, Eugen-Olsen J, Kristiansen TB. Severe acute respiratory syndrome – a new coronavirus from the Chinese dragon’s lair. Scand. J. Immunol. 58(3), 277–284 (2003).
  • Chan CH, Chan Y, Shieh HK et al. Phylogenetic analysis of influenza B virus in Taiwan, 1997 to 2001. J. Microbiol. Immunol. Infect. 37(3), 135–144 (2004).
  • Chopra I. Antibiotic resistance in Staphylococcus aureus: concerns, causes and cures. Expert Rev. Anti-infect. Ther. 1(1), 45–55 (2003).
  • Mansky LM. HIV mutagenesis and the evolution of antiretroviral drug resistance. Drug Resist. Update 5(6), 219–223 (2002).
  • Berzofsky JA, Terabe M, Oh S et al. Progress on new vaccine strategies for the immunotherapy and prevention of cancer. J. Clin. Invest. 113(11), 1515–1525 (2004).
  • Prescott SL, Jones CA. An update of immunotherapy for specific allergies. Curr. Drug Targets Inflamm. Allergy 1(1), 65–75 (2002).
  • Cope AP, Feldmann M. Emerging approaches for the therapy of autoimmune and chronic inflammatory disease. Curr. Opin. Immunol. 16(6), 780–786 (2004).
  • Zhang W, Yang H, Kong X et al. Inhibition of respiratory syncytial virus infection with intranasal siRNA nanoparticles targeting the viral NS1 gene. Nature Med. 11(1), 56–62 (2005).
  • De Giovanni C, Nicoletti G, Landuzzi L et al. Immunoprevention of HER-2/neu transgenic mammary carcinoma through an interleukin-12-engineered allogeneic cell vaccine. Cancer Res. 64(11), 4001–4009 (2004).
  • McDevitt H. Specific antigen vaccination to treat autoimmune disease. Proc. Natl Acad. Sci. USA 101(Suppl. 2), 14627–14630 (2004).
  • Brusic V, Petrovsky N. Immunoinformatics – the new kid in town. Novartis Found. Symp. 254, 3–13 (2003).
  • Rammensee HG. Immunoinformatics: bioinformatic strategies for better understanding of immune function. Introduction. Novartis Found. Symp. 254, 1–2 (2003).
  • Brusic V, Zeleznikow J, Petrovsky N. Molecular immunology databases and data repositories. J. Immunol. Methods 238(1–2), 17–28 (2000).
  • Galperin MY. The molecular biology database collection: 2005 update. Nucleic Acids Res. 33, D5–D24 (2005).
  • Brusic V, Millot M, Petrovsky N, Gendel SM, Gigonzac O, Stelman SJ. Allergen databases. Allergy 58(11), 1093–1100 (2003).
  • Haux R, Ammenwerth E, Herzog W, Knaup P. Healthcare in the information society. A prognosis for the year 2013. Int. J. Med. Inform. 66(1–3), 3–21 (2002).
  • Hasman A, Safran C, Takeda H. Quality of healthcare: informatics foundations. Methods Inf. Med. 42(5), 509–518 (2003).
  • McDonald S. Indigenous transplant outcomes in Australia: what the ANZDATA registry tells us. Nephrology (Carlton) 9(Suppl. 4), S138–S143 (2004).
  • DiMichele DM, Kroner BL. The North American Immune Tolerance Registry: practices, outcomes, outcome predictors. Thromb. Haemost. 87(1), 52–57 (2002).
  • Bencsath M, Blaskovits A, Borvendeg J. Biomolecular cytokine therapy. Pathol. Oncol. Res. 9(1), 24–29 (2003).
  • Girardi M, Knobler R, Edelson R. Selective immmunotherapy through extracorporeal photochemotherapy: yesterday, today, and tomorrow. Hematol. Oncol. Clin. North Am. 17(6), 1391–1403 (2003).
  • Merrill SJ. Computational models in immunological methods: an historical review. J. Immunol. Methods 216(1–2), 69–92 (1998).
  • Eskin E, Agichtein E. Combining text mining and sequence analysis to discover protein functional regions. Pac. Symp. Biocomput. 288–299 (2004).
  • Glenisson P, Coessens B, Van Vooren S, Mathys J, Moreau Y, De Moor B. TXTGate: profiling gene groups with text-based information. Genome Biol. 5(6), R43 (2004).
  • Karopka T, Scheel T, Bansemer S, Glass A. Automatic construction of gene relation networks using text mining and gene expression data. Med. Inform. Internet Med. 29(2), 169–183 (2004).
  • Brusic V, Petrovsky N, Gendel SM, Millot M, Gigonzac O, Stelman SJ. Computational tools for the study of allergens. Allergy 58(11), 1083–1092 (2003).
  • Lefranc MP. IMGT-ONTOLOGY and IMGT databases, tools and Web resources for immunogenetics and immunoinformatics. Mol. Immunol. 40(10), 647–660 (2004).
  • Lefranc MP, Giudicelli V, Kaas Q et al. IMGT, the international ImMunoGeneTics information system®. Nucleic Acids Res. 33, D593–D597 (2005).
  • Giudicelli V, Chaume D, Lefranc MP. IMGT/V-QUEST, an integrated software for immunoglobulin and T-cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Res. 32, W435–W440 (2004).
  • Monod MY, Giudicelli V, Chaume D, Lefranc MP. IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T-cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 20, I379–I385 (2004).
  • Kaas Q, Ruiz M, Lefranc MP. IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T-cell receptor and MHC structural data. Nucleic Acids Res. 32, D208–D210 (2004).
  • Brusic V, Bajic VB, Petrovsky N. Computational methods for prediction of T-cell epitopes – a framework for modelling, testing, and applications. Methods 34(4), 436–443 (2004).
  • Hakenberg J, Nussbaum AK, Schild H et al. MAPPP: MHC class I antigenic peptide processing prediction. Appl. Bioinformatics 2(3), 155–158 (2003).
  • Saxova P, Buus S, Brunak S, Kesmir C. Predicting proteasomal cleavage sites: a comparison of available methods. Int. Immunol. 15(7), 781–787 (2003).
  • Doytchinova I, Hemsley S, Flower DR. Transporter associated with antigen processing preselection of peptides binding to the MHC: a bioinformatic evaluation. J. Immunol. 173(11), 6813–6819 (2004).
  • Petrovsky N, Brusic V. Virtual models of the HLA class I antigen processing pathway. Methods 34(4), 429–435 (2004).
  • Bian H, Hammer J. Discovery of promiscuous HLA-II-restricted T-cell epitopes with TEPITOPE. Methods 34(4), 468–475 (2004).
  • De Groot AS, Jesdale B, Martin W et al. Mapping cross-clade HIV-1 vaccine epitopes using a bioinformatics approach. Vaccine 21(27–30), 4486–4504 (2003).
  • Doytchinova IA, Guan P, Flower DR. Quantitative structure-activity relationships and the prediction of MHC supermotifs. Methods 34(4), 444–453 (2004).
  • Srinivasan KN, Zhang GL, Khan AM, August JT, Brusic V. Prediction of class I T-cell epitopes: evidence of presence of immunological hot spots inside antigens. Bioinformatics 20(Suppl. 1), I297–I302 (2004).
  • Chao DL, Davenport MP, Forrest S, Perelson AS. A stochastic model of cytotoxic T-cell responses. J. Theor. Biol. 228(2), 227–240 (2004).
  • Borghans JAM, Beltman JB, De Boer RJ. MHC polymorphism under host–pathogen coevolution. Immunogenetics 55, 732–739 (2004).
  • Shahaf G, Allman D, Cancro MP, Mehr R. Screening of alternative models for transitional B-cell maturation. Int. Immunol. 16(8), 1081–1090 (2004).
  • Bernaschi M, Castiglione F. Design and implementation of an immune system simulator. Comput. Biol. Med. 31(5), 303–331 (2001).
  • Yates A, Chan CC, Callard RE, George AJ, Stark J. An approach to modelling in immunology. Brief Bioinform. 2(3), 245–257 (2001).
  • Castiglione F, Poccia F, D’Offizi G, Bernaschi M. Mutation, fitness, viral diversity, and predictive markers of disease progression in a computational model of HIV Type 1 infection. AIDS Res. Hum. Retroviruses 20(12), 1314–1323 (2004).
  • Schonbach C, Kowalski-Saunders P, Brusic V. Data warehousing in molecular biology. Brief Bioinform. 1(2), 190–198 (2000).
  • Hu H, Brzeski H, Hutchins J et al. Biomedical informatics: development of a comprehensive data warehouse for clinical and genomic breast cancer research. Pharmacogenomics 5(7), 933–941 (2004).
  • Sanchez W, Gilman B, Kher M, Lagou S, Covitz P. caGRID White Paper (cancer biomedical informatics grid prototype project). National Cancer Institute Center for Bioinformatics (NCICB), USA. July 23 (2004).
  • Koenig-Hoffmann K, Bonin-Debs AL, Boche I et al. High throughput functional genomics: identification of novel genes with tumor suppressor phenotypes. Int. J. Cancer 20, 113(3), 434–439 (2005).
  • Oh P, Li Y, Yu J et al. Subtractive proteomic mapping of the endothelial surface in lung and solid tumours for tissue-specific therapy. Nature 429(6992), 629–635 (2004).
  • Camp RL, Dolled-Filhart M, Rimm DL. X-tile: a new bio-informatics tool for biomarker assessment and outcome-based cut-point optimization. Clin. Cancer Res. 10(21), 7252–7259 (2004).
  • Glynne RJ, Watson SR. The immune system and gene expression microarrays – new answers to old questions. J. Pathol. 195(1), 20–30 (2001).
  • Novellino L, Castelli C, Parmiani G. A listing of human tumor antigens recognized by T-cells: March 2004 update. Cancer Immunol. Immunother. 54(3), 187–207 (2005).
  • Dalgleish AG. Cancer vaccines as a therapeutic strategy. Expert Rev. Vaccines 3(6), 665–668 (2004).
  • Motta S, Brusic V. Mathematical modelling of the immune system. In: Modelling in Molecular Biology. Ciobanu G, Rozenberg G (Eds), Natural Computing Series, Springer Verlag, Germany, 193–218 (2004).
  • Persson L, Bartlett M. Notifiable Diseases Database system: review and development strategy. NSW Public Health Bull. 15(1–2), 10–12 (2004).
  • Ferdinand S, Valetudie G, Sola C, Rastogi N. Data mining of Mycobacterium tuberculosis complex genotyping results using mycobacterial interspersed repetitive units validates the clonal structure of spoligotyping-defined families. Res. Microbiol. 155, 647–654 (2004).
  • Kiechle FL, Zhang X, Holland-Staley CA. The -omics era and its impact. Arch. Pathol. Lab. Med. 128, 1337–1345 (2004).
  • Bodrossy L, Sessitsch A. Oligonucleotide microarrays in microbial diagnostics. Curr. Opin. Microbiol. 7(3), 245–254 (2004).
  • Mora M, Veggi D, Santini L, Pizza M, Rappuoli R. Reverse vaccinology. Drug Discov. Today 8(10), 459–464 (2003).
  • De Groot AS, Berzofsky JA. From genome to vaccine – new immunoinformatics tools for vaccine design. Methods 34(4), 425–428 (2004).
  • Kellam P, Holzerlandt R, Gramoustianou E, Jenner R, Kwan A. Viral bioinformatics: computational views of host and pathogen. Novartis Found. Symp. 254, 234–247 (2003).
  • Wodarz D. Mathematical models of HIV and the immune system. Novartis Found. Symp. 254, 193–207 (2003).
  • Marino S, Kirschner DE. The human immune response to Mycobacterium tuberculosis in lung and lymph node. J. Theor. Biol. 227(4), 463–486 (2004).
  • Young K, Frodsham A, Doumbo OK et al. Inverse associations of human leukocyte antigen and malaria parasite types in two West African populations. Infect. Immun. 73(2), 953–955 (2005).
  • Holcombe M. Computational models of cells and tissues: machines, agents and fungal infection. Brief Bioinform. 2(3), 271–278 (2001).
  • Davies DH, Liang X, Hernandez JE et al. Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc. Natl Acad. Sci. USA 102(3), 547–552 (2005).
  • Rota PA, Oberste MS, Monroe SS et al. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300(5624), 1394–1399 (2003).
  • Scarselli M, Giuliani MM, Adu-Bobie J, Pizza M, Rappuoli R. The impact of genomics on vaccine design. Trends Biotech. 23(2), 84–91 (2005).
  • De Groot AS, Rappuoli R. Genome-derived vaccines. Expert Rev. Vaccines 3(1), 59–76 (2004).
  • Sette A, Fleri W, Peters B, Sathiamurthy M, Bui HH, Wilson S. A roadmap for the immunomics of category A-C pathogens. Immunity (2005) (In Press).
  • Locher CP, Soong NW, Whalen RG, Punnonen J. Development of novel vaccines using DNA shuffling and screening strategies. Curr. Opin. Mol. Ther. 6(1), 34–39 (2004).
  • Petrovsky N, Silva D, Brusic V. The future for computational modelling and prediction systems in clinical immunology. Novartis Found. Symp. 254, 23–32 (2003).
  • Stadler MB, Stadler BM. Allergenicity prediction by protein sequence. FASEB J. 17(9), 1141–1143 (2003).
  • Soeria-Atmadja D, Zorzet A, Gustafsson MG, Hammerling U. Statistical evaluation of local alignment features predicting allergenicity using supervised classification algorithms. Int. Arch. Allergy Immunol. 133(2), 101–112 (2004).
  • Li, KB, Issac P, Krishnan A. Predicting allergenic proteins using wavelet transform. Bioinformatics 20(16), 2572–2578 (2004).
  • Fiers MW, Kleter GA, Nijland H, Peijnenburg AA, Nap JP, van Ham RC. Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines. BMC Bioinformatics 5(1), 133 (2004).
  • Gendel SM. Bioinformatics and food allergens. J. AOAC Int. 87(6), 1417–1422 (2004).
  • Niederberger V, Valenta R. Genetically modified allergens. Immunol. Allergy Clin. North Am. 24(4), 727–738 (2004).
  • Antonelli A, Tuomi T, Nannipieri M et al. Autoimmunity to CD38 and GAD in Type I and Type II diabetes: CD38 and HLA genotypes and clinical phenotypes. Diabetologia 45(9), 1298–1306 (2002).
  • Royle P, Bain L, Waugh N. Systematic reviews of epidemiology in diabetes: finding the evidence. BMC Med. Res. Methodol. 5(1), 2 (2005).
  • Burren OS, Healy BC, Lam AC et al. Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics. Hum. Genomics 1(2), 98–109 (2004).
  • Weinstock-Guttman B, Jacobs LD, Brownscheidle CM et al. Multiple sclerosis characteristics in African American patients in the New York State Multiple Sclerosis Consortium. Mult. Scler. 9(3), 293–298 (2003).
  • Lund IK, Andersen HS, Iversen LF et al. Structure-based design of selective and potent inhibitors of protein-tyrosine phosphatase beta. J. Biol. Chem. 279(23), 24226–24235 (2004).
  • Flynn JC, McCormick DJ, Brusic V et al. Pathogenic human thyroglobulin peptides in HLA-DR3 transgenic mouse model of autoimmune thyroiditis. Cell. Immunol. 229(2), 79–85 (2004).
  • Teo YM, Wang X, Ng YK. GLAD: a system for developing and deploying large-scale bioinformatics grid. Bioinformatics (2005) (In Press).
  • Srinivasan KN, Brusic V, August JT. New technologies for vaccine development. Drug Dev. Res. 62, 383–392 (2004).
  • Kantor AB, Alters SE, Cheal K, Dietz LJ. Immune systems biology: immunoprofiling of cells and molecules. Biotechniques 36(3), 520–524 (2004).
  • Liang H, Cordova SE, Kieft TL, Rogelj S. A highly sensitive immuno-PCR assay for detecting Group A Streptococcus. J. Immunol. Methods 279(1–2), 101–110 (2003).
  • Liu F, Guttikonda S, Suresh MR. Bispecific monoclonal antibodies against a viral and an enzyme: utilities in ultrasensitive virus ELISA and phage display technology. J. Immunol. Methods 274(1–2), 115–127 (2003). Pappalardo F, Lollini PL, Castiglione F, Motta S. Modeling and simulation of cancer immunoprevention vaccine. Bioinformatics (2005) (In Press).

Websites

  • PubMed www.ncbi.nlm.nih.gov/PubMed (Accessed April 2005)
  • IMGT Bloc-notes http://imgt.cines.fr (Accessed April 2005)
  • International Federation of Pharmaceutical Manufacturers and Associations. Joint position on the disclosure of clinical trial information via clinical trial registries and databases. January 2005 www.efpia.org/4_pos/sci_regu/Clinicaltrials2005.pdf (Accessed April 2005)
  • SYFPEITHI www.syfpeithi.de (Accessed April 2005)
  • PREDBALB/c research.i2r.a-star.edUSg/predBalbc (Accessed April 2005)
  • RANKPEP mif.dfci.harvard.edu/Tools/rankpep.html (Accessed April 2005)
  • BIMAS www.bimas.cit.nih.gov/molbio/hla_bind (Accessed April 2005)
  • Allergen Nomenclature www.allergen.org (Accessed April 2005)
  • ExPASy Proteomics Server www.expasy.org (Accessed April 2005)

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.