Genomics and vaccine development

Animal Diseases/prevention & control; Animals; Drug Design; Genomics; Oligonucleotide Array Sequence Analysis; Proteomics; Vaccines/immunology; Veterinary Medicine/methods/trends

Abstract :

[en] The current explosion in new high-throughput technologies arising from microbial and animal genomics studies is enabling the analysis of the genome, transcriptome, and proteome and offers the opportunity to gain a better understanding of the molecular pathways underlying pathogen biology, the host immune system, and host-pathogen interactions. These new tools can be applied to veterinary pathogens to overcome some of the current hurdles in the discovery of highly effective vaccines for farmed livestock and poultry.

Disciplines :

Veterinary medicine & animal health

Author, co-author :

Gay, Cyril; United States Department of Agriculture, Agricultural Research Service, National Program Staff, Animal Production and Protection, Beltsville, MD, USA.

Zuerner, Richard

Bannantine, John P.

Lillehoj, Hyun

Zhu, James

Green, Ronnie

Pastoret, Paul-Pierre ; Université de Liège - ULiège > Médecine vétérinaire et santé animale

Language :

English

Title :

Genomics and vaccine development

Publication date :

2007

Journal title :

Revue Scientifique et Technique. Office International des Epizooties

ISSN :

0253-1933

eISSN :

1608-0637

Publisher :

Office International des Epizooties (OIE), Paris, France

Volume :

Issue :

Pages :

49-67

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

https://doc.oie.int/dyn/portal/index.seam?page=alo&aloId=30640

Available on ORBi :

since 13 September 2019

Statistics

Number of views

27 (0 by ULiège)

Number of downloads

0 (0 by ULiège)

More statistics

Scopus citations^®

Scopus citations^®
without self-citations

OpenCitations

Bibliography

Baskin C.R., Garcia-Sastre A., Tumpey T.M., Bielefeldt-Ohmann H., Carter V.S., Nistal-Villan E. & Katze M.G. (2004). - Integration of clinical data, pathology, and cDNA microarrays in influenza virus-infected pigtailed macaques (Macaca nemestrina). J. Virol., 78 (19), 10420-10432.
Blake D.P., Hesketh P., Archer A., Carroll F., Smith A.L. & Shirley M.W. (2004). - Parasite genetics and the immune host: recombination between antigenic types of Eimeria maxima as an entree to the identification of protective antigens. Molec. biochem. Parasitol., 138 (1), 143-152.
Blake D.P., Shirley M.W. & Smith A.L. (2006). - Genetic identification of antigens protective against coccidia. Parasite Immunol., 28 (7), 305-314.
Bloom B.R. & Murray C.J. (1992). - Tuberculosis: commentary on a reemergent killer. Science, 257 (5073), 1055-1064.
Blythe M.J. & Flower D.R. (2005). - Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci., 14 (1), 246-248.
Boyce J.D., Wilkie I., Harper M., Paustian M.L., Kapur V., & Adler B. (2002). - Genomic scale analysis of Pasteurella multocida gene expression during growth within the natural chicken host. Infect. Immun., 70 (12), 6871-6879.
Bricker B.J., Ewalt D.R. & Hailing S.M. (2003). - Brucella 'HOOF-Prints': strain typing by multi-locus analysis of variable number tandem repeats (VNTRs). BMC Microbiol., 3, 15.
Brosch R., Gordon S.V., Buchrieser C., Pym A.S., Gamier T., and Cole S.T. (2000). - Comparative genomics uncovers large tandem chromosomal duplications in Mycobacterium bovis BCG Pasteur. Yeast, 17 (2), 111-123.
Brown P.O. & Botstein D. (1999). - Exploring the new world of the genome with DNA microarrays.supply Nature Genet., 21 (1 suppl), 33-37.
Brusic V., Bajic V.B. & Petrovsky N. (2004). - Computational methods for prediction of T-cell epitopes - a framework for modelling, testing, and applications. Methods, 34 (4), 436-443.
Bulach D.M., Zuerner R.L., Wilson P., Seemann T., McGrath A., Cullen P.A., Davis J., Johnson M., Kuczek E., Alt D.P., Peterson-Burch B., Coppel R.L., Rood J.I., Davies J.K. & Adler B. (2006). - Genome reduction in Leptospira borgpetersenii reflects limited transmission potential. Proc. natl Acad. Sci. USA, 103 (39), 14560-14565.
Caoili S.E. (2006). - A structural-energetic basis for B-cell epitope prediction. Protein Pept. Lett., 13 (7), 743-751.
Carrillo C., Tulman E.R., Delhon G., Lu Z., Carreno A., Vagnozzi A., Kutish G.F. & Rock D.L. (2005). - Comparative genomics of foot-and-mouth disease virus. J. Virol., 79 (10), 6487-6504.
Chain P.S., Comerci D.J., Tolmasky M.E., Larimer F.W., Malfatti S.A., Vergez L.M., Aguero F., Land M.L., Ugalde R.A. & Garcia E. (2005). - Whole-genome analyses of speciation events in pathogenic Brucellae. Infect. Immun., 73 (12), 8353-8361.
Cohen P., Bouaboula M., Bellis M., Baron V., Jbilo O., Poinot-Chazel C., Galiegue S., Hadibi E.H. & Casellas P. (2000). - Monitoring cellular responses to Listeria monocytogenes with oligonucleotide arrays. J. biol. Chem., 275 (15), 11181-11190.
Cole S.T., Brosch R., Parkhill J., Gamier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. 3rd, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R., Devlin K., Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L., Oliver K., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton J., Squares R., Squares S., Sulston J.E., Taylor K., Whitehead S. & Barrell B.G. (1998). -Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature, 393 (6685), 537-544.
Collins F.S., Green E.D., Guttmacher A.E., & Guyer M.S. (2003). - A vision for the future of genomics research. Nature, 422 (6934), 835-847.
Cummings C.A. & Relman D.A. (2000). - Using DNA microarrays to study host-microbe interactions. Emerg. infect. Dis., 6 (5), 513-525.
Cunningham M.W (2000). - Pathogenesis of group A streptococcal infections. Clin. Microbiol. Rev., 13 (3), 470-511.
Dahlquist K.D., Salomonis N., Vranizan K., Lawlor S.C. & Conklin B. R. (2002). - GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature Genet., 31 (1), 19-20.
Dalloul R.A. & Lillehoj H.S. (2006). - Poultry coccidiosis: recent advancements in control measures and vaccine development. Expert. Rev. Vaccines, 5 (1), 143-163.
Dalloul R.A., Bliss T.W., Hong Y.H., Ben-Chouikha I., Park D.W., Keeler C.L. & Lillehoj H.S. (2007). - Unique responses of the avian macrophage to different species of Eimeria. Molec. Immunol., 44 (4), 558-566.
DelVecchio V.G., Kapatral V., Redkar R.J., Patra G., Mujer C., Los T., Ivanova N., Anderson I., Bhattacharyya A., Lykidis A., Reznik G., Jablonski L., Larsen N., D'Souza M., Bernal A., Mazur M., Goltsman E., Selkov E., Elzer P.H., Hagius S., O'Callaghan D., Letesson J.J., Haselkorn R., Kyrpides N. & Overbeek R. (2002). - The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc. natl Acad. Sci. USA, 99 (1), 443-448.
Doytchinova I.A., Guan P. & Flower D.R. (2004). - Identifiying human MHC supertypes using bioinformatic methods. J. Immunol., 172 (7), 4314-4323.
Draghici S. (2003). - Data analysis tools for DNA microarrays. Chapman & Hall/CRC, Boca Raton.
Eckmann L., Smith J.R., Housley M.P., Dwinell M.B. & Kagnoff M.F. (2000). - Analysis by high density cDNA arrays of altered gene expression in human intestinal epithelial cells in response to infection with the invasive enteric bacteria Salmonella. J. biol. Chem., 275 (19), 14084-14094.
Esposito J.J., Sammons S.A., Frace A.M., Osborne J.D., Olsen-Rasmussen M., Zhang M., Govil D., Damon I.K., Kline R., Laker M., Li Y., Smith G.L., Meyer H., Leduc J.W. & Wohlhueter R.M. (2006). - Genome sequence diversity and clues to the evolution of variola (smallpox) virus. Science, 313 (5788), 807-812.
Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., Bult C.J., Tomb J.F., Dougherty B.A., Merrick J.M., et al. (1995). - Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269 (5223), 496-512.
Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J., DeBoy R., Dodson R., Gwinn M., Haft D., Hickey E., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M., Salzberg S.L., Delcher A., Utterback T., Weidman J., Khouri H., Gill J., Mikula A., Bishai W., Jacobs Jr W.R., Venter J.C. & Fraser C.M. (2002). - Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacteriol., 184 (19), 5479-5490.
Flower D.R. (2003). - Databases and data mining for computational vaccinology. Curr. Opin. Drug Discov. Devel., 6 (3), 396-400.
Gamberini M., Gomez R.M., Atzingen M.V., Martins E.A., Vasconcellos S.A., Romero E.C., Leite L.C., Ho P.L. & Nascimento A.L. (2005). - Whole-genome analysis of Leptospira interrogans to identify potential vaccine candidates against leptospirosis. FEMS Microbiol. Lett., 244 (2), 305-313.
Gao L.Y., Pak M., Kish R., Kajihara K. & Brown E.J. (2006). - A mycobacterial operon essential for virulence in vivo and invasion and intracellular persistence in macrophages. Infect. Immun., 74 (3), 1757-1767.
Gamier T., Eiglmeier K., Camus J.C., Medina N., Mansoor H., Pryor M., Duthoy S., Grondin S., Lacroix C., Monsempe C., Simon S., Harris B., Atkin R., Doggett J., Mayes R., Keating L., Wheeler P.R., Parkhill J., Barrell B.G., Cole S.T., Gordon S.V. & Hewinson R.G. (2003). - The complete genome sequence of Mycobacterium bovis. Proc. natl Acad. Sci. USA, 100 (13), 7877-7882.
Geysen H.M., Meloen R.H. & Barteling S.J. (1984). - Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid. Proc. natl Acad. Sci. USA, 81 (13), 3998-4002.
Geysen H.M., Barteling S.J. & Meloen R.H. (1985). - Small peptides induce antibodies with a sequence and structural requirement for binding antigen comparable to antibodies raised against the native protein. Proc. natl Acad. Sci. USA, 82 (1), 178-182.
Gibbs R.A., Weinstock G., Kappes S.M., Schook L.B., Skow L. & Womack J. (2002). - Bovine genomic sequencing initiative: De-humanizing the cattle genome. Available at:http://www.genome.gov/Pages/Research/Sequencing/ SeqProposals/BovSeq.pdf.
Glass E.J. (2004). - Genetic variation and responses to vaccines. Anim. Hlth Res. Rev., 5 (2), 197-208.
Green R.D., Qureshi M.A. & Long J.A. (2005). - Charting the road map for long-term USDA efforts in agricultural animal genomics: summary of the USDA Animal Genomics Workshop, September 2004. USDA Mimeo (18 pp.).
Gulukota K. & DeLisi C. (1996). - HLA allele selection for designing peptide vaccines. Genet. Anal, 13 (3), 81-86.
Hailing S.M., Peterson-Burch B.D., Bricker B.J., Zuerner R.L., Qing Z., Li L.L., Kapur V., Alt D.P. & Olsen S.C. (2005). -Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis. J. Bacterial, 187 (8), 2715-2726.
Hans D., Young P.R. & Fairlie D.P. (2006). - Current status of short synthetic peptides as vaccines. Med. Chem., 2 (6), 627-646.
Haste Andersen P., Nielsen M. & Lund O. (2006). -Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci., 15 (11), 2558-2567.
Hawken R.J., Beattie C.W. & Schook L.B. (1998). - Resolving the genetics of resistance to infectious diseases. In Genetic resistance to animal diseases. Rev. sci. tech. Off. int. Epiz., 17 (1), 17-25.
Huntley J.F., Stabel J.R., Paustian M.L., Reinhardt T.A. & Bannantine J.P. (2005). - Expression library immunization confers protection against Mycobacterium avium subsp. paratuberculosis infection. Infect. Immun., 73 (10), 6877-6884.
International Chicken Genome Consortium (2004). -Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695-716.
International HapMap Consortium (2005). - A haplotype map of the human genome. Nature, 437, 1299-1320.
Johnston S.A. & Barry M.A. (1997). - Genetic to genomic vaccination. Vaccine, 15 (8), 808-809.
Kappes S.M., Green R.D. & Van Tassell C.P. (2006). - Sequencing the bovine genome and implications for future research. In Proc. 8th World Congress on Genetics Applied to Livestock Production. Belo Horizonte, Brazil.
Karaca G., Anobile J., Downs D., Burnside J. & Schmidt C.J. (2004). - Herpesvirus of turkeys: microarray analysis of host gene responses to infection. Virology, 318 (1), 102-111.
Korber B., LaBute M. & Yusim K. (2006). - Immunoinformatics comes of age. PLoS comput. Biol., 2 (6), e71.
Kroemer G., Guillemot F. & Auffray C. (1990). - Genetic organization of the chicken MHC. Immunol Res., 9 (1), 8-19.
Kumanovics A., Takada T. & Lindahl K.F. (2003). - Genomic organization of the mammalian MHC. Annu. Rev. Immunol., 21, 629-657.
Le Fleche P., Jacques I., Grayon M., Al Dahouk S., Bouchon P., Denoeud F., Nockler K., Neubauer H., Guilloteau L.A. & Vergnaud G. (2006). - Evaluation and selection of tandem repeat loci for a Brucella MLVA typing assay. BMC Microbiol., 6, 9.
Li L., Bannantine J.P., Zhang Q., Amonsin A., May B.J., Alt D., Banerji N., Kanjilal S. & Kapur V. (2005). - The complete genome sequence of Mycobacterium avium subspecies paratuberculosis. Proc. natl Acad. Sci. USA, 102 (35), 12344-12349.
Lillehoj H.S., Kim C.H., Keeler Jr. C.L. & Zhang S. (2007). -Immunogenomic approaches to study host immunity to enteric pathogens. Poult. Sci. (in press).
Liu H.C., Cheng H.H., Tirunagaru V., Sofer L. & Burnside J. (2001). - A strategy to identify positional candidate genes conferring Marek's disease resistance by integrating DNA microarrays and genetic mapping. Anim. Genet., 32 (6), 351-359.
Lo M., Bulach D.M., Powell D.R., Haake D.A., Matsunaga J., Paustian M.L., Zuerner R.L. & Adler B. (2006). - Effects of temperature on gene expression patterns in Leptospira intenogans serovar Lai as assessed by whole-genome microarrays. Infect. Immun., 74 (10), 5848-5859.
McSparron H., Blythe M.J., Zygouri C., Doytchinova I.A. & Flower D.R. (2003). - JenPep: a novel computational information resource for immunobiology and vaccinology. J. chem. Inf. Comput. Sci., 43 (4), 1276-1287.
Majed Z., Bellenger E., Postic D., Pourcel C., Baranton G. & Picardeau M. (2005). - Identification of variable-number tandem-repeat loci in Leptospira interrogans sensu stricto. J. clin. Microbiol., 43 (2), 539-545.
Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S. Chen Y.J., Chen Z., Dewell S.B., Du L., Fierro J.M., Gomes X.V., Godwin B.C., He W., Helgesen S., Ho C.H., Irzyk G.P., Jando S.C., Alenquer M.L., Jarvie T.P., Jirage K.B., Kim J.B., Knight J.R., Lanza J.R., Leamon J.H., Lefkowitz S.M., Lei M., Li J., Lohman K.L., Lu H., Makhijani V.B., McDade K.E., McKenna M.P., Myers E.W., Nickerson E., Nobile J.R., Plant R., Puc B.P., Ronan M.T., Roth G.T., Sarkis G.J., Simons J.F., Simpson J.W., Srinivasan M., Tartaro K.R., Tomasz A., Vogt K.A., Volkmer G.A., Wang S.H., Wang Y., Weiner M.P., Yu P., Begley R.F. & Rothberg J.M. (2005). - Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437 (7057), 376-380.
Marsh I.B., Bannantine J.P., Paustian M.L., Tizard M.L., Kapur V. & Whittington R.J. (2006). - Genomic comparison of Mycobacterium avium subsp. paratuberculosis sheep and cattle strains by microarray hybridization. J. Bacteriol., 188 (6), 2290-2293.
May B.J., Zhang Q., Li L.L., Paustian M.L., Whittam T.S. & Kapur V. (2001). - Complete genomic sequence of Posteurella multocida, Pm70. Proc. natl Acad. Sci. USA, 98 (6), 3460-3465.
Min W., Lillehoj H.S., Kim S., Zhu J.J., Beard H., Alkharouf N. & Matthews B.F. (2003). - Profiling local gene expression changes associated with Eimeria maxima and Eimeria acervulina using cDNA microarray. Appl. Microbiol. Biotechnol., 62 (4), 392-399.
Min W., Lillehoj H.S., Ashwell C.M., van Tassell C.P., Dalloul R.A., Matukumalli L.K., Han J.Y. & Lillehoj E.P. (2005). - Expressed sequence tag analysis of Eimeria-stimulated intestinal intraepithelial lymphocytes in chickens. Molec. Biotechnol., 30 (2), 143-150.
Moreau V., Granier C., Villard S., Laune D. & Molina F. (2006). - Discontinuous epitope prediction based on mimotope analysis. Bioinformatics, 22 (9), 1088-1095.
Mostowy S., Tsolaki A.G., Small P.M. & Behr M.A. (2003). - The in vitro evolution of BCG vaccines. Vaccine, 21 (37-30), 4270-4274.
Musser J.M. & DeLeo F.R. (2005). - Toward a genome-wide systems biology analysis of host-pathogen interactions in group A Streptococcus. Am. J. Pathol., 167 (6), 1461-1472.
Nagy G., Danino V., Dobrindt U., Pallen M., Chaudhuri R., Emody L., Hinton J.C. & Hacker J. (2006). - Down-regulation of key virulence factors makes the Salmonella enterica serovar Typhimurium rfaH mutant a promising live-attenuated vaccine candidate. Infect. Immun., 74 (10), 5914-5925.
Nascimento A.L., Ko A.I., Martins E.A., Monteiro-Vitorello C.B., Ho P.L., Haake D.A., Verjovski-Almeida S., Hartskeerl R.A., Marques M.V., Oliveira M.C., Menck C.F., Leite L.C., Carrer H., Coutinho L.L., Degrave W.M., Dellagostin O.A., El-Dorry H., Ferro E.S., Ferro M.I., Furlan L.R., Gamberini M., Giglioti E.A., Goes-Neto A., Goldman G.H., Goldman M.H., Harakava R., Jeronimo S.M., Junqueira-de-Azevedo I.L., Kimura E.T., Kuramae E.E., Lemos E.G., Lemos M.V., Marino C.L., Nunes L.R., de Oliveira R.C., Pereira G.G., Reis M.S., Schriefer A., Siqueira W.J., Sommer P., Tsai S.M., Simpson A.J., Ferro J.A., Camargo L.E., Kitajima J.P., Setubal J.C. & Van Sluys M.A. (2004). - Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis. J. Bacteriol., 186 (7), 2164-2172.
Newman M.J., Truax R.E., French D.D., Dietrich M.A., Franke D. & Stear M.J. (1996). - Evidence for genetic control of vaccine-induced antibody responses in cattle. Vet. Immunol. Immunopathol., 50 (1-2), 43-54.
Nielsen M., Lundegaard C., Worning P., Hvid C.S., Lamberth K., Buus S., Brunak S. & Lund O. (2004). -Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach. Bioinformatics, 20 (9), 1388-1397.
O'Neill R.G., Woolliams J.A., Glass E.J., Williams J.L. & Fitzpatrick J.L. (2006). - Quantitative evaluation of genetic and environmental parameters determining antibody response induced by vaccination against bovine respiratory syncytial virus. Vaccine, 24 (18), 4007-4016.
Parkhill J., Sebaihia M., Preston A., Murphy L.D., Thomson N., Harris D.E., Holden M.T., Churcher C.M., Bentley S.D., Mungall K.L., Cerdeno-Tarraga A.M., Temple L., James K., Harris B., Quail M.A., Achtman M., Atkin R., Baker S., Basham D., Bason N., Cherevach I., Chillingworth T., Collins M., Cronin A., Davis P., Doggett J., Feltwell T., Goble A., Hamlin N., Hauser H., Holroyd S., Jagels K., Leather S., Moule S., Norberczak H., O'Neil S., Ormond D., Price C., Rabbinowitsch E., Rutter S., Sanders M., Saunders D., Seeger K., Sharp S., Simmonds M., Skelton J., Squares R., Squares S., Stevens K., Unwin L., Whitehead S., Barrell B.G. & Maskell D.J. (2003). - Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet., 35 (1), 32-40.
Partidos C.D. & Steward M.W. (2002). - Mimotopes of viral antigens and biologically important molecules as candidate vaccines and potential immunotherapeutics. Comb. Chem. high Throughput Screen., 5 (1), 15-27.
Paulsen I.T., Seshadri R., Nelson K.E., Eisen J.A., Heidelberg J.F., Read T.D., Dodson R.J., Umayam L., Brinkac L.M., Beanan M.J., Daugherty S.C., Deboy R.T., Durkin A.S., Kolonay J.F., Madupu R., Nelson W.C., Ayodeji B., Kraul M., Shetty J., Malek J., Van Aken S.E., Riedmuller S., Tettelin H., Gill S.R., White O., Salzberg S.L., Hoover D.L., Lindler L.E., Hailing S.M., Boyle S.M. & Fraser C.M. (2002). - The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc. natl Acad. Sci. USA, 99 (20), 13148-13153.
Paustian M.L., Kapur V. & Bannantine J.P. (2005). - Comparative genomic hybridizations reveal genetic regions within the Mycobacterium avium complex that are divergent from Mycobacterium avium subsp. paratuberculosis isolates. J. Bacteriol., 187 (7), 2406-2415.
Pizza M., Scarlato V., Masignani V., Giuliani M.M., Arico B., Comanducci M., Jennings G.T., Baldi L. Bartolini E., Capecchi B., Galeotti C.L., Luzzi E., Manetti R., Marchetti E., Mora M., Nuti S., Ratti G., Santini L., Savino S., Scarselli M., Storni E., Zuo P., Broeker M., Hundt E., Knapp B., Blair E., Mason T., Tettelin H., Hood D.W., Jeffries A.C., Saunders N.J., Granoff D.M., Venter J.C., Moxon E.R., Grandi G. & Rappuoli R. (2000). - Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science, 287 (5459), 1816-1820.
Pizzi E., Cortese R. & Tramontano A. (1995). - Mapping epitopes on protein surfaces. Biopolymers, 36 (5), 675-680.
Pym A.S., Brodin P., Brosch R., Huerre M. & Cole S.T. (2002). - Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti. Molec. Microbiol., 46 (3), 709-717.
Quackenbush J. (2002). - Microarray data normalization and transformation. Nature Genet., 32 (Suppl.), 496-501.
Rappuoli R. (2000). - Reverse vaccinology. Curr. Op. Microbiol., 3 (5), 445-450.
Rappuoli R. (2001). - Reverse vaccinology, a genome-based approach to vaccine development. Vaccine, 19 (17-19), 2688-2691.
Read T.D., Salzberg S.L., Pop M., Shumway M., Umayam L., Jiang L., Holtzapple, E., Busch, J.D. et al. (2002). -Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science, 296 (5575), 2028-2033.
Reche PA. & Reinherz E.L. (2003). - Sequence variability analysis of human class I and class II MHC molecules: functional and structural correlates of amino acid polymorphisms. J. molec. Biol., 331 (3), 623-641.
Reche P.A. & Reinherz E.L. (2005). - PEPVAC: a web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands. Nucleic Acids Res., 33 (web server issue), W138-142.
Reid S.D., Green N.M., Buss J.K., Lei B. & Musser J.M. (2001). - Multilocus analysis of extracellular putative virulence proteins made by group A Streptococcus: population genetics, human serologic response, and gene transcription. Proc. natl Acad. Sci. USA, 98 (13), 7552-7557.
Ren S.X., Fu G., Jiang X.G., Zeng R., Miao Y.G., Xu H., Zhang Y.X., Xiong H., Lu G., Lu L.F., Jiang H.Q., Jia J., Tu Y.F., Jiang J.X., Gu W.Y., Zhang Y.Q., Cai Z., Sheng H.H., Yin H.F., Zhang Y., Zhu G.F., Wan M., Huang H.L., Qian Z., Wang S.Y., Ma W., Yao Z.J., Shen Y., Qiang B.Q., Xia Q.C., Guo X.K., Danchin A., Saint Girons I., Somerville R.L., Wen Y.M., Shi M.H., Chen Z., Xu J.G. & Zhao G.P. (2003). - Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature, 422 (6934), 888-893.
Rosinha G.M., Freitas D.A., Miyoshi A., Azevedo V., Campos E., Cravero S.L., Rossetti O., Splitter G. & Oliveira S.C. (2002). - Identification and characterization of a Brucella abortus ATP-binding cassette transporter homolog to Rhizobium meliloti ExsA and its role in virulence and protection in mice. Infect. Immun., 70 (9), 5036-5044.
Saha S. & Raghava G.P. (2006). - Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins, 65 (1), 40-48.
Salaun L., Merien F., Gurianova S., Baranton G. & Picardeau M. (2006). - Application of multilocus variable-number tandem-repeat analysis for molecular typing of the agent of leptospirosis J. clin. Microbiol., 44 (11), 3954-3962.
Scarselli M., Giuliani M.M., Adu-Bobie J., Pizza M. & Rappuoli R. (2005). - The impact of genomics on vaccine design. Trends Biotechnol., 23 (2), 84-91.
Sebaihia M., Preston A., Maskell D.J., Kuzmiak H., Connell T.D., King N.D., Orndorff P.E., Miyamoto D.M. et al. (2006). - Comparison of the genome sequence of the poultry pathogen Bordetella avium with those of B. bronchiseptica, B. pertussis, and B. parapertussis reveals extensive diversity in surface structures associated with host interaction. J. Bacteriol., 188 (16), 6002-6015.
Serruto D. & Rappuoli R. (2006). - Post-genomic vaccine development. FEBS Lett., 580 (12), 2985-2992.
Setubal J.C., Reis M., Matsunaga J. & Haake D.A. (2006). -Lipoprotein computational prediction in spirochaetal genomes. Microbiology, 152 (Pt 1), 113-121.
Sidney J., del Guercio M.F., Southwood S., Engelhard V.H., Appella E., Rammensee H.G., Falk K., Rotzschke O., Takiguchi M., Kubo R.T. et al. (1995). - Several HLA alleles share overlapping peptide specificities. J. Immunol., 154 (1), 247-259.
Slack A.T., Dohnt M.F., Symonds M.L. & Smythe L.D. (2005). - Development of a Multiple-Locus Variable Number of Tandem Repeat Analysis (MLVA) for Leptospira interrogans and its application to Leptospira interrogans serovar Australis isolates from Far North Queensland, Australia. Ann. clin. Microbiol. Antimicrob., 4 (10), 10.
Slack A.T., Symonds M., Dohnt M. & Smythe L. (2006). -An improved multiple-locus variable number of tandem repeats analysis for Leptospira interrogans serovar Australis: a comparison with fluorescent amplified fragment length polymorphism analysis and its use to redefine the molecular epidemiology of this serovar in Queensland, Australia. J. med. Microbiol., 55 (Pt II), 1549-1557.
Sollner J. (2006). - Selection and combination of machine learning classifiers for prediction of linear B-cell epitopes on proteins. J. mol. Recognit., 19 (3), 209-214.
Sollner J. & Mayer B. (2006). - Machine learning approaches for prediction of linear B-cell epitopes on proteins. J. mol. Recognit., 19 (3), 200-208.
Sorensen A.L., Nagai S., Houen G., Andersen P. & Andersen A.B. (1995). - Purification and characterization of a low-molecular-mass T-cell antigen secreted by Mycobacterium tuberculosis. Infect. Immun., 63 (5), 1710-1717.
Southern E., Mir K. & Shchepinov M. (1999). - Molecular interactions on microarrays. Nature Genet., 21 (1 suppl.), 5-9.
Stoughton R.B. (2005). - Applications of DNA microarrays in biology. Annu. Rev. Biochem., 74, 53-82.
Sumby P., Whitney A.R., Graviss E.A., DeLeo F.R. & Musser J.M. (2006). - Genome-wide analysis of group a streptococci reveals a mutation that modulates global phenotype and disease specificity. PLoS Pathog., 2 (1), e5.
Welsch J.A., Moe G.R., Rossi R., Adu-Bobie J., Rappuoli R. & Granoff D.M. (2003). - Antibody to genome-derived neisserial antigen 2132, a Neisseria meningitidis candidate vaccine, confers protection against bacteremia in the absence of complement-mediated bactericidal activity. J. infect. Dis., 188 (11), 1730-1740.
Whatmore A.M., Shankster S.J., Perrett L.L., Murphy T.J., Brew S.D., Thirlwall R.E., Cutler S.J. & MacMillan A.P. (2006). - Identification and characterization of variable-number tandem-repeat markers for typing of Brucella spp. J. clin. Microbiol., 44 (6), 1982-1993.
Williams R. B. (1999). - A compartmentalised model for the estimation of the cost of coccidiosis to the world's chicken production industry. Int. J. Parasitol., 29 (8), 1209-1229.
Wong G.K., Liu B., Wang J., Zhang Y., Yang X., Zhang Z., Meng Q., Zhou J., Li D., Zhang J., Ni P., Li S., Ran L., Li H., Zhang J., Li R., Li S., Zheng H., Lin W., Li G., Wang X., Zhao W., Li J., Ye C., Dai M., Ruan J., Zhou Y., Li Y., He X., Zhang Y., Wang J., Huang X., Tong W., Chen J., Ye J., Chen C., Wei N., Li G., Dong L., Lan F., Sun Y., Zhang Z., Yang Z., Yu Y., Huang Y., He D., Xi Y., Wei D., Qi Q., Li W., Shi J., Wang M., Xie F., Wang J., Zhang X., Wang P., Zhao Y., Li N., Yang N., Dong W., Hu S., Zeng C., Zheng W., Hao B., Hillier L.W., Yang S.P., Warren W.C., Wilson R.K., Brandstrom M., Ellegren H., Crooijmans R.P., van der Poel J.J., Bovenhuis H., Groenen M.A., Ovcharenko I., Gordon L., Stubbs L., Lucas S., Glavina T., Aerts A., Kaiser P., Rothwell L., Young J.R., Rogers S., Walker B.A., van Hateren A., Kaufman J., Bumstead N., Lamont S.J., Zhou H., Hocking P.M., Morrice D., de Koning D.J., Law A., Bartley N., Burt D.W., Hunt H., Cheng H.H., Gunnarsson U., Wahlberg P. et al. (2004). - A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature, 432 (7018), 717-722.
Zhang G.L., Petrovsky N., Kwoh C.K., August J.T. & Brusic V. (2006). - PREDTAP: a system for prediction of peptide binding to the human transporter associated with antigen processing. Immunome Res., 2, 3.
Zhu H., Cong J.P., Mamtora G., Gingeras T. & Shenk T. (1998). - Cellular gene expression altered by human cytomegalovirus: global monitoring with oligonucleotide arrays. Proc. natl Acad. Sci. USA, 95 (24), 14470-14475.