Volume 17, Number 2—February 2011
Research
Next-Generation Sequencing of Coccidioides immitis Isolated during Cluster Investigation
Figure 3
References
- Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Res. 2008;18:324–30. DOIPubMedGoogle Scholar
- Cummings CA, Bormann Chung CA, Fang R, Barker M, Brzoska PM, Williamson P, Whole-genome typing of Bacillus anthracis isolates by next-generation sequencing accurately and rapidly identifies strain-specific diagnostic polymorphisms. Forensic Sci Int Genet. 2009;2:300–1. DOIGoogle Scholar
- Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK, Chantratita N, Evolution of MRSA during hospital transmission and intercontinental spread. Science. 2010;327:469–74. DOIPubMedGoogle Scholar
- Galgiani JN, Ampel NM, Blair Je, Catanzaro A. Johnson RH, Stevens DA, et al. Coccidioidomycosis. Clin Infect Dis. 2005;41:1217–23. DOIPubMedGoogle Scholar
- Blair JE. Coccidioidomycosis in patients who have undergone transplantation. Ann N Y Acad Sci. 2007;1111:365–76. DOIPubMedGoogle Scholar
- The Broad Institute Coccidioides Group [updated 2010 Mar 31] [cited 2010 Apr 1]. http://www.broadinstitute.org/annotation/genome/coccidioides_group/GenomeDescriptions.html#iCoccidioidesimmitisiRS
- Homer N, Merriman B, Nelson SF. BFAST: an alignment tool for large scale genome resequencing. PLoS ONE. 2009;4:e7767. DOIPubMedGoogle Scholar
- Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res. 2009;19:1722–31. DOIPubMedGoogle Scholar
- Colvin SNP. Caller–TGen [updated 2010 Mar 31] [cited 2010 Apr 1]. http://public.tgen.org/merge-pileup
- Short Read Archive–NCBI [updated 2008 Nov 5] [cited 2010 Feb 15]. http://www.ncbi.nlm.nih.gov/sra/SRX022538?report=full
- Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, 1000 Genome Project Data Processing Subgroup. The sequence alignment/map (SAM) format and SAMtools. Bioinformatics. 2009;25:2078–9. DOIPubMedGoogle Scholar
- Kurtz S, Phillippy A, Delcher A, Smoot M, Shumway M, Antonescu C, Versatile and open software for comparing large genomes. Genome Biol. 2004;5:R12. DOIPubMedGoogle Scholar
- Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596–9. DOIPubMedGoogle Scholar
- Nei M, Kumar S. Molecular evolution and phylogenetics. New York: Oxford University Press; 2000. p. 132.
- Keckich DW, Blair JE, Vikram HR. Coccidioides fungemia in six patients, with a review of the literature. Mycopathologia. 2010;170:107–15. Epub 2010 Mar 25. DOIPubMedGoogle Scholar
- Taylor JW, Geiser DM, Burt A, Koufopanou V. The evolutionary biology and population genetics underlying fungal strain typing. Clin Microbiol Rev. 1999;12:126–46.PubMedGoogle Scholar
- Fisher MC, Koenig GL, White TJ, San-Blas G, Negroni R, Alvarez IG, Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration. Proc Natl Acad Sci U S A. 2001;98:4558–62. DOIPubMedGoogle Scholar
- Jewell K, Cheshire R, Cage GD. Genetic diversity among clinical Coccidioides spp. isolates in Arizona. Med Mycol. 2008;46:449–55. DOIPubMedGoogle Scholar
- Keim P, Van Ert M, Pearson T, Vogler A, Hyunh L, Wagner D. Anthrax molecular epidemiology and forensics: using different markers for the appropriate evolutionary scales. Infect Genet Evol. 2004;4:205–13. DOIPubMedGoogle Scholar
- Pearson T, Okinaka RT, Foster JT, Keim P. Phylogenetic understanding of clonal populations in an era of whole genome sequencing. Infect Genet Evol. 2009;9:1010–9. DOIPubMedGoogle Scholar
- Pearson T, Giffard P, Beckstrom-Sternberg S, Auerbach R, Hornstra H, Tuanyok A, Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer BMC Biol. 2009; 18;7:78. PMID: 19922616
- Burt A, Carter DA, Koenig GL, White TJ, Taylor JW. Molecular markers reveal cryptic sex in the human pathogen Coccidioides immitis. Proc Natl Acad Sci U S A. 1996;93:770–3. DOIPubMedGoogle Scholar
- Greub G, Kebbi-Beghdadi C, Bertelli C, Collyn F, Riederer BM, Yersin C, High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach. PLoS ONE. 2009;4:e8423. DOIPubMedGoogle Scholar
- Schielke A, Sachs K, Lierz M, Appel B, Jansen A, Johne R. Detection of hepatitis E virus in wild boars of rural and urban regions in Germany and whole genome characterization of an endemic strain. Virol J. 2009;14;6:58. PMID: 19442307
- Sanabani SS, Pastena ER, Kleine Neto W, Barreto CC, Ferrari KT, Kalmar EM, Near full-length genome analysis of low prevalent human immunodeficiency virus type 1 subclade F1 in São Paulo, Brazil. Virol J. 2009;16;6:78. PMID: 19531216
- Liu J, Xiao H, Lei F, Zhu Q, Qin K, Zhang XW, Highly pathogenic H5N1 influenza virus infection in migratory birds. Science. 2005;309:1206. DOIPubMedGoogle Scholar
- Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, Corneveaux JJ, Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods. 2008;5:887–93. DOIPubMedGoogle Scholar
- Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25. DOIPubMedGoogle Scholar
- Schatz MC. CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics. 2009;25:1363–9. DOIPubMedGoogle Scholar
- Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biol. 2009;10:R134. DOIPubMedGoogle Scholar
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