Immunoinformatics: An integrated scenario

Immunology

Volumn 131, Issue 2, 2010, Pages 153-168

  Tomar, Namrata ^a   De, Rajat K ^a  

^a INDIAN STATISTICAL INSTITUTE   (India)

Author keywords

allergy; B cells; in silico models; major histocompatibility complex human leucocyte antigen; T cells

Indexed keywords

DNA VACCINE; EPITOPE; HLA ANTIGEN;

ADAPTIVE IMMUNITY; ALLERGY; B LYMPHOCYTE; COMPUTER MODEL; DATA BASE; IMMUNE SYSTEM; IMMUNOINFORMATICS; IMMUNOMICS; MACHINE LEARNING; MAJOR HISTOCOMPATIBILITY COMPLEX; MEDICAL INFORMATICS; MICROARRAY ANALYSIS; PRIORITY JOURNAL; REVIEW; T LYMPHOCYTE; VACCINE PRODUCTION;

ALLERGY AND IMMUNOLOGY; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; HUMANS; INTERNET;

EID: 77956319457     PISSN: 00192805     EISSN: 13652567     Source Type: Journal    
DOI: 10.1111/j.1365-2567.2010.03330.x     Document Type: Review

References (135)

1. Kimbrell DA, Beutler B. The evolution and genetics of innate immunity. Nat Rev Genet 2001 2 : 256 267.
2. Thomas K, Goldsby J, Osborne RA, Barbara A, Kuby J. Kuby Immunology, 6th edn. New York : WH Freeman and Co, 2006.
3. Korber B, LaBute M, Yusim K. Immunoinformatics comes of age. PLoS Comput Biol 2006 2 : 0484 0492.
4. Gardy JL, Lynn DJ, Brinkman FSL, Hancock REW. Enabling a systems biology approach to immunology: focus on innate immunity. Trends Immunol 2009 30 : 249 262.
5. Davies MN, Flower DR. Harnessing bioinformatics to discover new vaccine. Drug Discov Today 2007 12 : 389 395.
6. Ortutay C, Vihinen M. Immunome Knowledge base (IKB): an integrated service for immunome research. BMC Immunol 2009 10. doi:.
7. Sette A, Fleri W, Peters B, Sathiamurthy M, Bui HH. A roadmap for the immunomics of category A-C pathogens. Immunity 2005 22 : 155 161.
8. Groot ASDe. Immunomics: discovering new targets for vaccine and therapeutics. Drug Discov Today 2006 11 : 203 209.
9. Grainger DJ. Immunomics: principles and practice. IRTL 2004 2 : 1 6.
10. Yates A, Chan CCW, Callard RE, George AJT, Stark J. An approach to modelling in immunology. Brief Bioinform 2001 2 : 245 257.
11. Kaplan No, Everse J, Dixon Je, Stolzenbach Fe, Lee Cy, Lee Clt, Taylor Ss, Mosbach K. Purification and separation of pyridine nucleotide-linked dehydrogenases by affinity chromatography techniques. Proc Natl Acad Sci USA 1974 71 : 3450 3454.
12. Davey HM. Flow cytometric techniques for the detection of microorganisms. Methods Cell Sci 2004 24 : 91 7.
13. Durkin MM, Patricia A, Connolly PA, Wheat LJ. Comparison of radioimmunoassay and enzyme-linked immunoassay methods for detection of Histoplasma capsulatum var. capsulatum antigen. J Clin Microbiol 1997 35 : 2252 2255.
14. Ma H, Shieh KJ, Lee SL. Study of ELISA technique. Nat Sci 2006 4 : 36 7.
15. Nishimaki T, Sagawa K, Motogi S, Saito K, Morito T, Yoshida H, Kasukawa R. A competitive inhibition test of enzyme immunoassay for the anti-nRNP antibody. J Immunol Methods 1987 100 : 157 160.
16. Levine MA, Thornton P, Forman SJ et al. Positive Coombs test in Hodgkin's disease: significance and implications. Blood 1980 55 : 607 611.
17. Wanga B, Huaa RH, Tiana Z-J, Chena N-S, Zhaoa F-R, Liua T-Q, Wanga Y-F, Tong G-Z. Identification of a virus-specific and conserved B-cell epitope on NS1 protein of Japanese encephalitis virus. Virus Res 2009 141 : 90 5.
18. Admon A, Barnea E, Ziv T. Tumor antigens and proteomics from the point of view of the major histocompatibility complex peptides. Mol Cell Proteomics 2003 2 : 388 398.
19. Boon T, Coulie PG, den Eynde BV. Tumor antigens recognized by T cells. Immunol Today 1997 18 : 267 268.
20. Gubler DJ. Dengue and dengue hemorrhagic fever. Clin Microbiol Rev 1998 11 : 480 496.
21. Amin N, Aguilar A, Chamac ho F et al. Identification of dengue-specific B-cell epitopes by phage-display random peptide library. Malaysian J Med Sci 2009 16 : 4 14.
22. Wang Y. Immunostaining with dissociable antibody microarrays. Proteomics 2004 4 : 20 6.
23. Magdalena J, Odling J, Qiang PH, Martenn S, Joakin L, Uhlen M, Hammarstrom L, Nilsson P. Serum microarrays for large scale screening of protein levels. Mol Cell Proteomics 2005 4 : 1942 1947.
24. Sahin U, Tureci O, Pfreundschuh M. Serological identification of human tumor antigens. Curr Opin Immunol 1997 9 : 709 716.
25. Oelke M, Maus MV, Didiano D, June CH, Mackensen A, Schneck JP. Ex vivo induction and expansion of antigen-specific cytotoxic T cells by HLA-Ig coated artificial antigen-presenting cells. Nat Med 2003 9 : 619 624.
26. Groot DeAS, Sbai H, Aubin CS, Mcmurry J, Martin W. Immuno-informatics: mining genomes for vaccine components. Immunol Cell Biol 2002 80 : 225 269.
27. Quintana FJ, Hagedorn PH, Gad E, Yifat M, Eutan D, Cohen IR. Functional immunomics: microarray analysis of IgG autoantibody repertoires predicts the future response of mice to induced diabetes. Proc Natl Acad Sci USA 2004 101 : 14615 14621.
28. Sampson HA. Food allergy - accurately identifying clinical reactivity. Allergy 2005 60 : 19 24.
29. Vegvar de HEN, Robinson WH. Microarray profiling of antiviral antibodies for the development of diagnostics, vaccines, and therapeutics. J Clin Immunol 2004 111 : 196 201.
30. Henry ENdeV, RamaRao A, Lawrence S, Paul JU, Harriet LR, Robinson WH. Microarray profiling of antibody responses against simian-human immunodeficiency virus: postchallenge convergence of reactivities independent of host histocompatibility type and vaccine regimen. J Virol 2003 77 : 11125 11138.
31. Nahtman T, Jernberg A, Mahdavifar S, Zerweck J, Schutkowski M, Maeurer M, Reilly M. Validation of peptide epitope microarray experiments and extraction of quality data. J Immunol Methods 2007 328 : 1 13.
32. Braga-Neto UM, Marques ETA. From functional genomics to functional immunomics: new challenges, old problems, big rewards. PLoS Comput Biol 2006 2 : 651 662.
33. Peters B, Sidney J, Bourne P et al. The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol 2005 3 : 1361 1370.
34. Lynn DJ, Winsor GL, Chan C et al. InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 2008 4 : 1 11.
35. Barsky S, Gardy JL, Hancock R, Munzer T. Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics 2007 23 : 1040 1042.
36. Shanon P, Markiel A, Ozier O et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003 13 : 2498 2504.
37. Saha S, Bhasin M, Raghava GPS. Bcipep: a database of B-cell epitopes. BMC Genomics 2005 6. doi:.
38. Huang J, Honda W. CED: a conformational epitope. BMC Immunol 2006 7 : 7.
39. Schlessinger A, Ofran Y, Yachdav G, Rost B. Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res 2006 34 : D777 80.
40. Blythe MJ, Doytchinova IA, Darren R. JenPep: a database of quantitative functional peptide data for immunology. Bioinformatics 2002 18 : 434 439.
41. Rammensee HG, Bachmann J, Emmerich NPN, Bachor OA, Stevanovic S. SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 1999 50 : 213 219.
42. Feldhahn M, Donnes P, Thiel P, Kohlbacher O. FRED - a framework for T-cell epitope detection. Bioinformatics 2009 25 : 2758 2759.
43. ®. Nucleic Acids Res 2009 37 : D1006 12.
44. Lord P, Shah N, Sansone SA, Stephens S, Soldatova L (eds). The OBI Consortium. Modeling biomedical experimental processes with OBI, In : Proceedings of the 12th Annual Bio-Ontologies 35 Meeting. International Society for Computational Biology. Sweden : Stockholm 2009 41 4.
45. Mari A, Scalab E, Palazzob P, Ridolfib S, Zennarob D, Carabella G. Bioinformatics applied to allergy: allergen databases, from collecting sequence information to data integration. The Allergome platform as a model. Cell Immunol 2006 244 : 97 100.
46. Pomes A. Relevant B cell epitopes in allergic disease. Int Arch Allergy Immunol 2010 152 : 1 11.
47. Hoffman D, Lowenstein H, Marsh DG, Platts-Mills TAE, Thomas W. Allergen nomenclature. Bull World Health Organ 1994 72 : 796 806.
48. Kim C, Kwon S, Lee G, Lee H, Choi J, Kim Y, Hahn J. A database for allergenic proteins and tools for allergenicity prediction. Bioinformation 2009 3 : 344 345.
49. Ivanciuc O, Schein CH, Braun W. SDAP: database and computational tools for allergenic proteins. Nucleic Acids Res 2003 31 : 359 362.
50. Ortutay C, Siermala M, Vihinen M. ImmTree: database of evolutionary relationships of genes and proteins in the human immune system. Immunome Res 2007 3 : doi:.
51. Ortutay C, Vihinen M. Immunome: a reference set of genes and proteins for systems biology of the human immune system. Cell Immunol 2006 244 : 87 9.
52. Rannikko K, Ortutay C, Vihinen M. Immunity genes and their orthologs: a multi-species database. Int Immunol 2007 19 : 1361 1370.
53. Greenbaum JA, Andersen PH, Blythe M et al. Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit 2007 20 : 75 82.
54. Tong JC, Ren EC. Immunoinformatics: current trends and future directions. Drug Discov Today 2009 14 : 684 689.
55. Pellequer J, Westhof E, Regenmortel MV. Predicting the location of structure of continuous epitopes in proteins from their primary structure. Methods Enzymol 1991 203 : 176 201.
56. Parker J, Guo D, Hodges R. 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.
57. Chou PY, Fasman GD. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol 1978 47 : 45 148.
58. Levitt M. Conformational preferences of amino acids in globular proteins. Biochemistry 1978 17 : 4277 4285.
59. Emini E, Hughes J, Perlow D, Boger J. Induction of hepatitis A virus-neutralizing antibody by a virus specific synthetic peptide. J Virol 1985 55 : 836 839.
60. El-Manzalawy Y, Dobbs D, Honavar V. Predicting protective linear B-cell epitopes using evolutionary information. In : Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, Washington : IEEE Computer Society 2008 : 289 292.
61. Odorico M, Pellequer JL. BEPITOPE: predicting the location of continuous epitopes and patterns in protein. J Mol Recognit 2003 16 : 20 2.
62. Pellequer JL, Westhof E. PREDITOP: a program for antigenicity predictions. J Mol Graph 1993 11 : 204 210.
63. Saha S, Raghava GPS. BcePred: prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties. In : Nicosia G, Cutello V, Bentley PJ, Timis J eds. Artificial Immune Systems. Berlin/Heidelberg ICARIS Springer, LNCS 2004 3239 : 197 204.
64. Ghate AD, Bhagwat BU, Bhosle SG, Gadepalli SM, Kulkarni-Kale UD. Characterization of antibody-binding sites on proteins: development of a knowledge base and its applications in improving epitope prediction. Protein Pept Lett 2007 14 : 531 535.
65. Saha S, Raghava GPS. Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins 2006 65 : 40 8.
66. Sweredoski MJ, Baldi P. COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng Des Sel 2009 22 : 113 120.
67. Larsen JEP, Lund O, Nielsen M. Improved method for predicting linear B cell epitopes. Immunome Res 2006 doi:.
68. Toseland CP, Clayton DJ, McSparron H et al. AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res 2005 1. doi:.
69. Evans MC. Recent advances in immunoinformatics: application of in silico tools to drug development. Curr Opin Drug Discov Devel 2008 11 : 233 241.
70. Anderson Ph, Nielsen M, Lund O. Prediction of residues in discontinuous B cell epitopes using protein 3D structures. Protein Sci 2006 15 : 2558 2567.
71. Bublil EM, Mayrose NTFI, Penn O, Berman AR. Stepwise prediction of conformational discontinuous B-cell epitopes using the mapitope algorithm. Proteins 2007 68 : 294 304.
72. Sollner J, Grohmann R, Rapberger R, Perco P, Lukas A, Mayer B. Analysis and prediction of protective continuous B cell epitopes on pathogen proteins. Immunome Res 2008 4. doi:.
73. Kale KU, Bhosle S, Kolaskar AS. CEP: a conformational epitope prediction server. Nucleic Acids Res 2005 33 : W168 71.
74. Mayrose I, Penn O, Erez E et al. Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics 2007 23 : 3244 3246.
75. Moreau V, Granier C, Villard S, Laune D, Molina F. Discontinuous epitope prediction based on mimotope analysis. Bioinformatics 2006 22 : 1088 1095.
76. Huang J, Gutteridge A, Honda W, Kanehisa M. MIMOX: a web tool for phage display based epitope mapping. BMC Bioinformatics 2006 7. doi:.
77. Mayrose I, Shlomi T, Rubinstein ND, Gershoni JM, Ruppin E, Sharan R, Pupko T. Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res 2007 35 : 69 78.
78. Schreiber A, Humbert M, Benz A, Dietrich U. 3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins. J Comput Chem 2005 26 : 879 887.
79. Huang L, Dai Y. Direct prediction of T-cell epitopes using support vector machines with novel Sequence encoding schemes. J Bioinform Comput Biol 2006 4 : 93 107.
80. Bhasin M, Raghava GPS. Prediction of promiscuous and high-affinity mutated MHC binders. Hybrid Hybridomics 2003 22 : 229 234.
81. TAP : a system for prediction of peptide binding to the human transporter associated with antigen processing. Immunome Res 2006 2. doi:.
82. Neilsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, Buus S, Brunak S, Lund O. Reliable prediction of T-cell epitopes using networks with novel sequence representations. Protein Sci 2003 12 : 1007 1017.
83. Buus S, Stryhn A, Winther K, Kirkby N, Pedersen LO. Receptor-ligand interactions measured by an improved spun column chromatography technique. A high efficiency and high throughput size separation method. Biochim Biophys Acta 1995 1243 : 453 460.
84. Larsen MV, Lundegaard C, Lamberth K, Buss S, Lund O, Nielsen M. Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics 2007 8. doi:.
85. Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M. 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.
86. Brusic V, Rudy G, Honeyman M, Hammer J, Harrison L. Prediction of MHC class II-binding peptides using an evolutionary and artificial neural network. Bioinformatics 1998 14 : 121 130.
87. Miyata J. A User's Guide to PlaNet Version 5.6. Boulder : Computer Science Department, University of Colorado. 1991.
88. Nanni L. Machine learning algorithms for T-cell epitopes prediction. Neurocomputing 2006 69 : 866 868.
89. Bhasin M, Raghava GPS. Analysis and prediction of affinity of TAP binding peptides using cascade SVM. Protein Sci 2004 13 : 596 607.
90. Bhasin M, Raghava GPS. Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences. Nucleic Acids Res 2005 33 : W202 7.
91. Joachims T. Marking large-scale support vector machine learning practical. In : Scholkopf B, Burges CJC, Smola AJ, eds. Advances in Kernel Methods: Support Vector Learning. Cambridge, MA, USA : MIT Press, 1999 : 169 184.
92. Cost S, Salzberg S. A weighted nearest neighbor algorithm for learning with symbolic features. Mach Learn 1993 10 : 57 78.
93. Witten IH, Frank E. Data Mining: Practical Machine Learning Tools and Techniques with Java Implementations, 2nd edn. San Francisco : Morgan Kaufman, 1999.
94. Dorigo M, Maniezzo MV, Cambini AC. Ant system: optimization by a colony of cooperating agents. IEEE Trans Syst Man Cybern Part B 1996 26 : 29 41.
95. Flower DR. Towards in silico prediction of immunogenic epitopes. Trends Immunol 2003 24 : 667 674.
96. Bian H, Hammer H. Discovery of promiscuous HLA restricted T cell epitope with TEPITOPE. Methods 2004 34 : 468 475.
97. Kangueane P, Sakharkar MK. T epitope designer: HLA peptide binding prediction server. Bioinformation 2005 1 : 21 4.
98. Zhao B, Mathura VS, Ganapathy R, Moochhala S, Sakharkar MK, Kangneane P. A novel MHCp binding prediction model. Hum Immunol 2003 64 : 1123 1143.
99. Ponomarenko JV, Bui HH, Li W, Fusseder N, Bourne PE, Sette A, Peters B. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 2008 9. doi:.
100. Guan P, Doytchinova IA, Zygouri C, Flower DR. MHCPred: a server for quantitative prediction of peptide-MHC binding. Nucleic Acids Res 2003 31 : 3621 3624.
101. Schiewe AJ, Haworth IS. Structure based prediction of MHC-peptide association: algorithm comparison and approach to cancer vaccine design. J Mol Graph Model 2007 26 : 667 675.
102. Jojic N, Gomez MR, Heckerman D, Kadle C, Furman OS. Learning MHC-I peptide binding. Bioinformatics 2006 22 : e227 35.
103. Furman OS, Altuvia Y, Sette A, Margalit H. Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles. Protein Sci 2000 9 : 1838 1846.
104. Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 1996 256 : 623 644.
105. Altuvia Y, Margalit H. A structure-based approach for prediction of MHC-binding peptides. Methods 2004 34 : 454 459.
106. Singh H, Raghava GPS. Propred: prediction of HLA-DR binding sites. Trends Immunol 2001 17 : 1236 1237.
107. Sturniolo T, Bono E, Ding J et al. Generation of tissue-specific and promiscuous HLA ligand database using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol 1999 17 : 555 561.
108. Feldhahn M, Thiel P, Schuler MM, Hillen N, Stevanovic S, Rammensee HG, Ohlbacher O. EpiToolKit - a web server for computational immunomics. Nucleic Acids Res 2008 1 : W519 22.
109. Stadler MB, Stadler BM. Allergenicity prediction by protein sequence. FASEB J 2003 17 : 1141 1143.
110. Kong W, Tan TS, Tham L, Choo KW. Improved prediction of allergenicity by combination of multiple sequence motifs. In Silico Biol 2006 7 : 77 86.
111. Bjorklund AK, Atmadja SD, Zorzet A, Hammerling U, Gustafsson MG. Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins. Bioinformatics 2005 21 : 39 50.
112. Zorzet A, Gustafsson M, Hammerling U. Prediction of food protein allergenicity: a bioinformatic learning systems approach. In Silico Biol 2002 2 : 525 534.
113. Saha S, Raghava GPS. AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Res 2006 34 : W202 9.
114. Fiers MWEJ, Kleter GA, Nijland H, Peijnenburg AACM, Peter NJ, Ham RCHJV. Allermatch™, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines. BMC Bioinformatics 2004 5. doi:.
115. FAO/WHO. Allergenicity of Genetically Modified Foods. 2001 Available at http://www.who.int/foodsafety/publications/biotech/en/ec-jan2001.pdf.
116. FAO/WHO. Codex Principles and Guidelines on Foods Derived from Biotechnology. 2003 Available at ftp://ftp.fao.org/codex/standard/en/ CodexTextsBiotechFoods.pdf.
117. Cui J, Han LY, Li H, Ung CY, Tang ZQ, Zheng CJ, Cao ZW, Chen YZ. Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties. Mol Immunol 2007 44 : 514 520.
118. Barrio AM, Atmadja DS, Nistr A, Gustafsson MG, Hammerling U, Rudloff EB. EVALLER: a web server for in silico assessment of potential protein allergenicity. Nucleic Acids Res 2007 35 : 694 700.
119. Soeria-Atmadja D, Lundell T, Gustafsson MG, Hammerling U. Computational detection of allergenic proteins attains a new level of accuracy with in silico variable-length peptide extraction and machine learning. Nucleic Acids Res 2006 34 : 3779 3793.
120. Pizza M, Scarlato V, Masignani V et al. Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 2000 287 : 1816 1820.
121. Groot ASDe, Rappuoli R. Genome derived vaccines. Expert Rev Vaccines 2003 3 : 59 76.
122. Gallimore A, Hengartner H, Zinkernagel R. Hierarchies of antigen-specific cytotoxic T cell responses. Immunol Rev 1998 164 : 29 36.
123. Morris S, Kelly C, Howard A, X Li, Collins F. The immunogenicity of single and combination DNA vaccines against tuberculosis. Vaccine 2000 18 : 2155 2163.
124. Zhao B, Sakharkar KR, Lim CS, Kangueane P, Sakharkar MK. MHC-peptide binding prediction for epitope based vaccine design. Int J Integr Biol 2007 1 : 127 140.
125. Florea L, Haldorsson B, Kohlbacher O, Schwarty R, Hoffman S, Istrail S. Epitope prediction algorithm for peptide-based vaccine design. In Proceedings of the IEEE Computer Society Conference on Bioinformatics, Washington : IEEE Computer Society. 2003 : 17 26.
126. Doytchinova IA, Flower DR. VaxiJen: a server for prediction of protective antigens, tumor antigens and subunit vaccines. BMC Bioinformatics 2007 8. doi:.
127. Nagarajan H, Gupta R, Agarwal P, Scaria V, Pillai B. DyNAVacS: an integrative tool for optimized DNA vaccine design. Nucleic Acids Res 2006 34 : W264 6.
128. Vivona S, Bernante F, Filippini F. NERVE: new enhanced reverse vaccinology environment. BMC Biotechnol 2006 6. doi:.
129. Xiang Z, Todd T, Ku KP et al. VIOLIN: vaccine investigation and online information network. Nucleic Acids Res 2008 36 : D923 8.
130. Xianga Z, He Y. Vaxign: a web-based vaccine target design program for reverse vaccinology. Procedia in Vaccinology 2009 1 : 23 9.
131. Gong T, Cai Z. Visual modeling and simulation of adaptive immune system. In Proceedings of the 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference, Shanghai, China, 2005 6 : 6116 6119.
132. Kalita JK, Chandrashekar K, Hans R, Selvam P, Newell MK. Computational modelling and simulation of the immune system. Int J Bioinform Res Appl 2006 2 : 63 88.
133. Castiglione F, Liso A. The role of computational models of the immune system in designing vaccination strategies. Immunopharmacol Immunotoxicol 2005 27 : 417 432.
134. Vivona S, Gardy JL, Ramachandran S, Brinkman FSL, Raghava GPS, Flower DR, Filippini F. Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends Biotechnol 2008 26 : 190 200.
135. Daz P, Gillespie M, Krueger J, Prez J, Radebaugh A, Shearman T, Vo G, Wheatley C. A mathematical model of the immune system's response in obesity-related chronic inflammation. In : McNair/MAOP Summer Research Symposium, Virginia Tech, Blacksburg VA. 2008 2 : 26 45.