Erratum to: Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary [Genome Biol (2016), 17, 238], DOI: 10.1186/s13059-016-1108-8;Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary

Genome Biology

Volumn 17, Issue 1, 2016, Pages

  Brynildsrud, Ola ^a   Bohlin, Jon ^a   Scheffer, Lonneke ^a,b   Eldholm, Vegard ^a  

^a NORWEGIAN INSTITUTE OF PUBLIC HEALTH   (Norway)

^b HANZE UNIVERSITY OF APPLIED SCIENCES   (Netherlands)

Author keywords

Accessory genome; Annotation; Association; Bacteria; Genome wide association studies (GWAS); Genomics; Next generation sequencing (NGS); Pan genome; Prokaryote; Python; Whole genome sequencing (WGS)

Indexed keywords

GENE MUTATION; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMAN; LICENCE; NEXT GENERATION SEQUENCING; NONHUMAN; PROKARYOTE; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE; STRATIFICATION;

EID: 84997283916     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-016-1132-8     Document Type: Erratum

References (35)

1. Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P, Cheng L, et al. Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet. 2014;46(3):305-9.
2. Laabei M, Recker M, Rudkin JK, Aldeljawi M, Gulay Z, Sloan TJ, et al. Predicting the virulence of MRSA from its genome sequence. Genome Res. 2014;24(5):839-49.
3. Sheppard SK, Didelot X, Meric G, Torralbo A, Jolley KA, Kelly DJ, et al. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proc Natl Acad Sci. 2013;110(29):11923-7.
4. Desjardins CA, Cohen KA, Munsamy V, Abeel T, Maharaj K, Walker BJ, et al. Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance. Nat Genet. 2016;48(5):544-51.
5. Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, et al. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet. 2013;45(10):1183-9.
6. Earle SG, Wu C-H, Charlesworth J, Stoesser N, Gordon NC, Walker TM, et al. Identifying lineage effects when controlling for population structure improves power in bacterial association studies. Nat Microbiol. 2016;1:16041.
7. Hall BG. SNP-associations and phenotype predictions from hundreds of microbial genomes without genome alignments. PLoS One. 2014;9(2):e90490.
8. Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, et al. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci. 2015;112(27):E3574-81.
9. Lees JA, Vehkala M, Valimaki N, Harris SR, Chewapreecha C, Croucher NJ, Marttinen P, Davies MR, Steer AC, Tong SY, et al. Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. Nat Commun 2016;7:12797.
10. Chen PE, Shapiro BJ. The advent of genome-wide association studies for bacteria. Curr Opin Microbiol. 2015;25:17-24.
11. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev. 2005;15(6):589-94.
12. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A. 2005;102(39):13950-5.
13. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31(22):3691-3.
14. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559-75.
15. Jones E, Oliphant E, Peterson P, et al. SciPy: Open Source Scientific Tools for Python. 2001. http://www.scipy.org/. Accessed 21 Nov 2016.
16. Abdi H. The Bonferonni and Šidák corrections for multiple comparisons. Encyclopedia of measurement and statistics. 2007;3:103-7.
17. Wright SP. Adjusted p-values for simultaneous inference. Biometrics. 1992;48:1005-13.
18. Read AF, Nee S. Inference from binary comparative data. J Theor Biol. 1995;173(1):99-108.
19. Maddison WP. Testing character correlation using pairwise comparisons on a phylogeny. J Theor Biol. 2000;202(3):195-204.
20. Ridley M. The explanation of organic diversity: the comparative method and adaptations for mating. Oxford: Oxford University Press; 1983.
21. Maddison WP, FitzJohn RG. The unsolved challenge to phylogenetic correlation tests for categorical characters. Syst Biol. 2015;64(1):127-36.
22. Sadleir RW, Makovicky PJ. Cranial shape and correlated characters in crocodilian evolution. J Evol Biol. 2008;21(6):1578-96.
23. North BV, Curtis D, Sham PC. A note on the calculation of empirical P values from Monte Carlo procedures. Am J Hum Genet. 2002;71(2):439-41.
24. Dennis LS, Daniel H, Harry L, John LH, Donald HB, Barry H, et al. Linezolid versus vancomycin for the treatment of methicillin-resistant Staphylococcus aureus infections. Clin Infect Dis. 2002;34(11):1481-90.
25. Gu B, Kelesidis T, Tsiodras S, Hindler J, Humphries RM. The emerging problem of linezolid-resistant Staphylococcus. J Antimicrob Chemother. 2013;68(1):4-11.
26. Tewhey R, Gu B, Kelesidis T, Charlton C, Bobenchik A, Hindler J, et al. Mechanisms of linezolid resistance among coagulase-negative staphylococci determined by whole-genome sequencing. MBio. 2014;5(3):e00894-00814.
27. Shortridge VD, Flamm RK, Ramer N, Beyer J, Tanaka SK. Novel mechanism of macrolide resistance in Streptococcus pneumoniae. Diagn Microbiol Infect Dis. 1996;26(2):73-8.
28. Van Rijsbergen C. Information retrieval. dept. of computer science, university of glasgow. 1979. citeseer ist psu edu/vanrijsbergen79information html.
29. Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, et al. Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes. PLoS Genet. 2014;10(8):e1004547.
30. Crusoe MR, Alameldin HF, Awad S, Boucher E, Caldwell A, Cartwright R, et al. The khmer software package: enabling efficient nucleotide sequence analysis. F1000 Research. 2015;4:900.
31. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455-77.
32. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068-9.
33. Mendes RE, Deshpande LM, Bonilla HF, Schwarz S, Huband MD, Jones RN, et al. Dissemination of a pSCFS3-like cfr-carrying plasmid in Staphylococcus aureus and Staphylococcus epidermidis clinical isolates recovered from hospitals in Ohio. Antimicrob Agents Chemother. 2013;57(7):2923-8.
34. Cai JC, Hu YY, Zhou HW, Chen G-X, Zhang R. Dissemination of the same cfr-carrying plasmid among methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococcal isolates in China. Antimicrob Agents Chemother. 2015;59(6):3669-71.
35. Howden BP, Seemann T, Harrison PF, McEvoy CR, Stanton J-AL, Rand CJ, et al. Complete genome sequence of Staphylococcus aureus strain JKD6008, an ST239 clone of methicillin-resistant Staphylococcus aureus with intermediate-level vancomycin resistance. J Bacteriol. 2010;192(21):5848-9.