Integrative immunoinformatics for Mycobacterial diseases in R platform

Rupanjali Chaudhuri1, Deepika Kulshreshtha1, Muthukurussi Varieth Raghunandanan1, Srinivasan Ramachandran1
1CSIR-Institute of Genomics and Integrative Biology, Near Jubilee Hall, Mall Road, Delhi, 110 007, India

Tóm tắt

Từ khóa


Tài liệu tham khảo

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

Griffith DE (2010) Nontuberculous mycobacterial lung disease. Curr Opin Infect Dis 23:185–190

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

Koonin EV (2005) Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39:309–338

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

McCarthy AA (2005) Broad institute: bringing genomics to real-world medicine. Chem Biol 12:717–718

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/

Rappuoli R (2000) Reverse vaccinology. Curr Opin Microbiol 3:445–450

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

Saha S, Raghava GP (2007) Prediction methods for B-cell epitopes. Methods Mol Biol 409:387–394

Sette A, Rappuoli R (2010) Reverse vaccinology: developing vaccines in the era of genomics. Immunity 4:530–541

Singh H, Raghava GP (2001) ProPred: prediction of HLA-DR binding sites. Bioinformatics 17:1236–1237

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

Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B (2008) Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res 36(Web Server):W513–W518