The rise of a digital immune system

GigaScience

Volumn 1, Issue 4, 2012, Pages

  Schatz, Michael C ^a   Phillippy, Adam M ^b,c  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^b National Biodefense Analysis and Countermeasures Center   (United States)

^c Bldg 142   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; BIOTECHNOLOGY; COMPUTER MODEL; COMPUTER SYSTEM; DIGITAL IMMUNE SYSTEM; HUMAN; IMMUNE RESPONSE; IMMUNOSURVEILLANCE; INFORMATION PROCESSING; METAGENOMICS; NONHUMAN; NOTE; PRIORITY JOURNAL; PUBLIC HEALTH; SEQUENCE ANALYSIS;

EID: 84899704095     PISSN: None     EISSN: 2047217X     Source Type: Journal    
DOI: 10.1186/2047-217X-1-4     Document Type: Note

References (12)

1. Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 2010, 11(10):685-696. 10.1038/nrg2841, 20847746.
2. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature 2007, 449(7164):804-810. 10.1038/nature06244, 17943116.
3. Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Møller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011, 365(8):709-717. 10.1056/NEJMoa1106920, 3168948, 21793740.
4. Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach. Nat Rev Genet 2010, 11(7):476-486. 3321268, 20531367.
5. Schatz MC, Langmead B, Salzberg SL. Cloud computing and the DNA data race. Nat Biotech 2010, 28(7):691-693.
6. Mason CE, Elemento O. Faster sequencers, larger datasets, new challenges. Genome Biol 2012, 13(3):314. 10.1186/gb-2012-13-3-314, 22452984.
7. Curtis TP, Sloan WT, Scannell JW. Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 2002, 99(16):10494-10499. 10.1073/pnas.142680199, 124953, 12097644.
8. Hillman MJ, Rivailler P, Smagala J, De Graaf M, Burke DF, Fouchier RA, Pappas C, Alpuche-Aranda CM, López-Gatell H, Olivera H, López I, Myers CA, Faix D, Blair PJ, Yu C, Keene KM, Dotson PD, Boxrud D, Sambol AR, Abid SH, St George K, Bannerman T, Moore AL, Stringer DJ, Blevins P, Demmler-Harrison GJ, Ginsberg M, Kriner P, Waterman S, Smole S, Guevara HF, Belongia EA, Clark PA, Beatrice ST, Donis R, Katz J, Finelli L, Bridges CB, Shaw M, Jernigan DB, Uyeki TM, Smith DJ, Klimov AI, Cox NJ. Antigenic and genetic characteristics of swine-origin 2009 A(H1N1) influenza viruses circulating in humans. Science 2009, 325(5937):197-201. 10.1126/science.1176225, 3250984, 19465683.
9. Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen MJ, Wang J, Aepfelbacher M, Yang R. E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium: Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 2011, 365(8):718-724. 10.1056/NEJMoa1107643, 21793736.
10. Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V, Spiro DJ, Sitz J, Koo H, Bolotov P, Dernovoy D, Tatusova T, Bao Y, St George K, Taylor J, Lipman DJ, Fraser CM, Taubenberger JK, Salzberg SL. Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature 2005, 437(7062):1162-1166. 10.1038/nature04239, 16208317.
11. Wolf YI, Nikolskaya A, Cherry JL, Viboud C, Koonin E, Lipman DJ. Projection of seasonal influenza severity from sequence and serological data. PLoS Curr 2010, 2:RRN1200. 2998708, 21152078.
12. Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Gardete S, Tavares A, Day N, Lindsay JA, Edgeworth JD, de Lencastre H, Parkhill J, Peacock SJ, Bentley SD. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327(5964):469-474. 10.1126/science.1182395, 2821690, 20093474.