Integrative immunoinformatics for Mycobacterial diseases in R platform
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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Andersen PH, Nielsen M, Lund O (2006) Prediction of residues in discontinuous B cell epitopes using protein 3D structures. Protein Sci 15:2358–2367
Ansari FA, Kumar N, Bala Subramanyam M, Gnanamani M, Ramachandran S (2008) MAAP: malarial adhesins and adhesin-like proteins predictor. Proteins 70:659–666
Ariel N, Zvi A, Grosfeld H, Gat O, Inbar Y, Velan B, Cohen S, Shafferman A (2002) Search for potential vaccine candidate open reading frames in the Bacillus anthracis virulence plasmid pXO1: in silico and in vitro screening. Infect Immun 70:6817–6827
Armitige LY, Jagannath C, Wanger AR, Norris SJ (2000) Disruption of the genes encoding antigen 85A and antigen 85B of Mycobacterium tuberculosis H37Rv: effect on growth in culture and in macrophages. Infect Immun 68:767–778
Baddeley A, Dean A, Dias HM, Falzon D et al (2013) World Health Organization Global Tuberculosis Report. http://www.who.int/tb/publications/global_report/en/index.html . Accessed 1 November 2013
Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 30. J Mol Biol 340:783–795
Bradley P, Cowen L, Menke M, King J, Berger B (2001) BETAWRAP: successful prediction of parallel beta-helices from primary sequence reveals an association with many microbial pathogens. Proc Natl Acad Sci USA 98:14819–14824
Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothé BR, Chisari FV, Watkins DI, Sette A (2005) Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics 57:304–314
Chakravarti DN, Fiske MJ, Fletcher LD, Zagursky RJ (2000) Application of genomics and proteomics for identification of bacterial gene products as potential vaccine candidates. Vaccine 19:601–612
Chaudhuri R, Ahmed S, Ansari FA, Singh HV, Ramachandran S (2008) MalVac: database of malarial vaccine candidates. Malar J 7:184
Chaudhuri R, Ansari FA, Raghunandanan MV, Ramachandran S (2011) FungalRV: adhesin prediction and immunoinformatics portal for human fungal pathogens. BMC Genom 12:192
Dogra S, Narang T, Kumar B (2013) Leprosy–evolution of the path to eradication. Indian J Med Res 137:15–35
Fiers MW, Kleter GA, Nijland H, Peijnenburg AA, Nap JP, Van RC (2004) Allermatch, a webtool for the prediction of potential allergenicity according to current FAO/WHO Codex alimentarius guidelines. BMC Bioinform 5:133
Ioerger TR, Koo S, No EG, Chen X, Larsen MH, Jacobs WR Jr, Pillay M, Sturm AW, Sacchettini JC (2009) Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa. PLoS One 4:e7778
Katoch VM (2004) Infections due to non-tuberculous mycobacteria (NTM). Indian J Med Res 120:290–304
Kaufmann SH (2002) Protection against tuberculosis: cytokines, T cells, and macrophages. Ann Rheum Dis 61(Suppl 2):ii54–ii58
Kaufmann SH (2011) Fact and fiction in tuberculosis vaccine research: 10 years later. Lancet Infect Dis 11:633–640
Khan AM, Miotto O, Heiny AT, Salmon J, Srinivasan KN, Nascimento EJ, Marques ET Jr, Brusic V, Tan TW, August JT (2007) A systematic bioinformatics approach for selection of epitope-based vaccine targets. Cell Immunol 244:141–147
Kinhikar AG, Verma I, Chandra D, Singh KK, Weldingh K, Andersen P, Hsu T, Jacobs WR Jr, Laal S (2010) Potential role for ESAT6 in dissemination of M tuberculosis via human lung epithelial cells. Mol Microbiol 75:92–106
Kolaskar AS, Tongaonkar PC (1990) A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett 276:172–174
Kondrashov FA, Rogozin IB, Wolf YI and Koonin EV (2002) Selection in the evolution of gene duplications. Genome Biol 3:RESEARCH0008
Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580
Kulkarni-Kale U, Bhosle S and Kolaskar AS (2005) CEP: a conformational epitope prediction server. Nucleic Acids Res 33(Web Server issue):W168–W171
Lienhardt C, Glaziou P, Uplekar M, Lönnroth K, Getahun H, Raviglione M (2012) Global tuberculosis control: lessons learnt and future prospects. Nat Rev Microbiol 10:407–416
Lockwood DNJ (2007) Leprosy Clin Evid (Online) Apr 1; 2007 pii: 0915
Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M (2008) NetMHC-30: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res 36(Web Server):W509–W512
Maione D, Margarit I, Rinaudo CD, Masignani V, Mora M, Scarselli M, Tettelin H, Brettoni C, Iacobini ET, Rosini R et al (2005) Identification of a universal Group B streptococcus vaccine by multiple genome screen. Science 309:148–150
Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D and Bryant SH (2005) CDD: a Conserved Domain Database for protein classification. Nucleic Acids Res 192–196
Marinova D, Gonzola-Asensio J, Aguilo N, Martin C (2013) Recent developments in tuberculosis vaccines. Expert Rev Vaccines 12:1431–1438
Mayer KH, Dukes HC (2010) Synergistic pandemics: confronting the global HIV and tuberculosis epidemics. Clin Infect Dis 3:S67–S70
McShane H (2011) Tuberculosis vaccines: beyond bacille Calmette-Guerin. Philos Trans R Soc Lond B Biol Sci 366:2782–2789
Menozzi FD, Bischoff R, Fort E, Brennan MJ, Locht C (1998) Molecular characterization of the mycobacterial heparin-binding hemagglutinin, a mycobacterial adhesin. Proc Natl Acad Sci USA 13:12625–12630
Merle CS, Cunha SS, Rodrigues LC (2010) BCG vaccination and leprosy protection: review of current evidence and status of BCG in leprosy control. Expert Rev Vaccines 9:209–222
Mora M, Veggi D, Santini L, Pizza M, Rappuoli R (2003) Reverse vaccinology. Drug Discov Today 8:459–464
Moreno-Hagelsieb G, Latimer K (2008) Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics 24:319–324
Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, Bui HH, Grey H, Sette A (2006) A consensus epitope prediction approach identifies the breadth of murine T(CD8 +)-cell responses to vaccinia virus. Nat Biotechnol 24:817–819
Nackers F, Dramaix M, Johnson RC, Zinsou C, Robert A, de Biurrun Bakedano E, Glynn JR, Portaels F, Tonglet R (2006) BCG vaccine effectiveness against Buruli ulcer: a case-control study in Benin. Am J Trop Med Hyg 75:768–774
Parker KC, Bednarek MA, Coligan JE (1994) Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol 152:163–175
Patronov A, Doytchinova I (2013) T-cell epitope vaccine design by immunoinformatics. Open Biol 3:120139
Cooper PS, Lipshultz D, Matten WT, McGinnis SD, Pechous S, Romiti ML, Tao T, Valjavec-Gratian M, Sayers EW (2010) Education resources of the National Center for Biotechnology Information. Brief Bioinform 11:563–569
Pizza M, Scarlato V, Masignani V, Giuliani MM, Aricò B, Comanducci M, Jennings GT, Baldi L et al (2000) Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science 287:1816–1820
Ramachandran S, Chaudhuri R, Verma SP, Shah AR, Paul C, Chakraborty S, Puniya BL and Mandal RS (2011) Biological Data Modelling and Scripting in R, Systems and Computational Biology - Bioinformatics and Computational Modeling, Prof Ning-Sun Yang (Ed), InTech. http://www.intechopen.com/books/systems-and-computational-biology-bioinformatics-and-computational-modeling/biological-data-modelling-and-scripting-in-r
R Core Team (2013) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org/
Rehm A, Stern P, Ploegh HL, Tortorella D (2001) Signal peptide cleavage of a type I membrane protein, HCMV US11, is dependent on its membrane anchor. EMBO J 20:1573–1582
Ross BC, Czajkowski L, Hocking D, Margetts M, Webb E, Rothel L, Patterson M, Agius C, Camuglia S, Reynolds E, Littlejohn T, Gaeta B, Ng A, Kuczek ES, Mattick JS, Gearing D, Barr IG (2001) Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis. Vaccine 19:4135–4142
Sachdeva G, Kumar K, Jain P, Ramachandran S (2005) SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks. Bioinformatics 21:483–491
Saha S, Raghava GP (2006) AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Res W202–W209
Saha S, Raghava GP (2006b) Prediction of continuous b-cell epitopes in an antigen using Recurrent Neural Network. Proteins 65:40–48
Sette A, Rappuoli R (2010) Reverse vaccinology: developing vaccines in the era of genomics. Immunity 4:530–541
Stone AC, Wilbur AK, Buikstra JE, Roberts CA (2009) Tuberculosis and leprosy in perspective. Am J Phys Anthropol 49:66–94
Sweredoski MJ, Baldi P (2008) PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics 24:1459–1460
Thorpe C, Edwards L, Snelgrove R, Finco O, Rae A, Grandi G, Guilio R, Hussell T (2007) Discovery of a vaccine antigen that protects mice from Chlamydia pneumoniae infection. Vaccine 25:2252–2260
Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B (2010) The immune epitope database 20. Nucleic Acids Res 38(Database issue): D854–D862
Vivona S, Bernante F, Filippini F (2006) NERVE: new enhanced reverse vaccinology environment. BMC Biotechnol 6:35
Vivona S, Gardy JL, Ramachandran S, Brinkman FS, Raghava GP, Flower DR, Filippini F (2008) Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends Biotechnol 26:190–200
Waller EA, Roy A, Brumble L, Khoor A, Johnson MM, Garland JL (2006) The expanding spectrum of Mycobacterium avium complex-associated pulmonary disease. Chest 130:1234–1241
Wang P, Sidney J, Kim Y, Sette A, Lund O, Nielsen M, Peters B (2010) Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinform 11:568
Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FS (2010) PSORTb 30: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26:1608–1615