PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples-Reference-Cited by-同舟云学术

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PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples

Published:2014-09-05 Issue:1 Volume:2 Page:
ISSN:2049-2618
Container-title:Microbiome
language:en
Short-container-title:Microbiome

Author:

Hong Changjin,Manimaran Solaiappan,Shen Ying,Perez-Rogers Joseph F,Byrd Allyson L,Castro-Nallar Eduardo,Crandall Keith A,Johnson William Evan

Publisher

Springer Science and Business Media LLC

Subject

Microbiology (medical),Microbiology

Link

http://link.springer.com/content/pdf/10.1186/2049-2618-2-33.pdf

Reference22 articles.

1. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA, Bonazzi V, McEwen JE, Wetterstrand KA, Deal C, Baker CC, Di Francesco V, Howcroft TK, Karp RW, Lunsford RD, Wellington CR, Belachew T, Wright M, Giblin C, David H, Mills M, Salomon R, Mullins C, Akolkar B, Begg L, Davis C, Grandison L, Humble M, Khalsa J, NIH HMP Working Group, et al: The NIH human microbiome project. Genome Res. 2009, 19: 2317-2323.

2. Chen EC, Yagi S, Kelly KR, Mendoza SP, Tarara RP, Canfield DR, Maninger N, Rosenthal A, Spinner A, Bales KL, Schnurr DP, Lerche NW, Chiu CY: Cross-species transmission of a novel adenovirus associated with a fulminant pneumonia outbreak in a new world monkey colony. PLoS Pathog. 2011, 7: e1002155-10.1371/journal.ppat.1002155.

3. 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: Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med. 2011, 365: 718-724. 10.1056/NEJMoa1107643.

4. Snitkin ES, Zelazny AM, Thomas PJ, Stock F, Henderson DK, Palmore TN, Segre JA: Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med. 2012, 4: 148ra116-

5. Brady A, Salzberg SL: Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods. 2009, 6: 673-676. 10.1038/nmeth.1358.

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