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Results: 1 to 20 of 35

1.

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.

Koren S, Phillippy AM.

Curr Opin Microbiol. 2015 Feb;23C:110-120. doi: 10.1016/j.mib.2014.11.014. Epub 2014 Dec 1. Review.

PMID:
25461581
[PubMed - as supplied by publisher]
Free Article
2.

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.

Treangen TJ, Ondov BD, Koren S, Phillippy AM.

Genome Biol. 2014;15(11):524.

PMID:
25410596
[PubMed - in process]
Free PMC Article
3.

Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923.

Treangen TJ, Maybank RA, Enke S, Friss MB, Diviak LF, Karaolis DK, Koren S, Ondov B, Phillippy AM, Bergman NH, Rosovitz MJ.

Genome Announc. 2014 Nov 6;2(6). pii: e01110-14. doi: 10.1128/genomeA.01110-14.

PMID:
25377701
[PubMed]
Free PMC Article
4.

High-coverage sequencing and annotated assemblies of the budgerigar genome.

Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, Xiong Y, Zhang Y, Zhou S, Schwartz DC, Schatz M, Aboukhalil R, Fedrigo O, Bukovnik L, Wang T, Wray G, Rasolonjatovo I, Winer R, Knight JR, Koren S, Warren WC, Zhang G, Phillippy AM, Jarvis ED.

Gigascience. 2014 Jul 8;3:11. doi: 10.1186/2047-217X-3-11. eCollection 2014.

PMID:
25061512
[PubMed]
Free PMC Article
5.

Automated ensemble assembly and validation of microbial genomes.

Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM.

BMC Bioinformatics. 2014 May 3;15:126. doi: 10.1186/1471-2105-15-126.

PMID:
24884846
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Complete Closed Genome Sequences of Four Mannheimia varigena Isolates from Cattle with Shipping Fever.

Harhay GP, Murray RW, Lubbers B, Griffin D, Koren S, Phillippy AM, Harhay DM, Bono J, Clawson ML, Heaton MP, Chitko-McKown CG, Smith TP.

Genome Announc. 2014 Feb 13;2(1). pii: e00088-14. doi: 10.1128/genomeA.00088-14.

PMID:
24526648
[PubMed]
Free PMC Article
7.

Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever.

Harhay GP, McVey DS, Koren S, Phillippy AM, Bono J, Harhay DM, Clawson ML, Heaton MP, Chitko-McKown CG, Korlach J, Smith TP.

Genome Announc. 2014 Feb 13;2(1). pii: e00084-14. doi: 10.1128/genomeA.00084-14.

PMID:
24526647
[PubMed]
Free PMC Article
8.

Reducing assembly complexity of microbial genomes with single-molecule sequencing.

Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM.

Genome Biol. 2013;14(9):R101.

PMID:
24034426
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

PMID:
23870653
[PubMed]
Free PMC Article
10.

Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle.

Harhay GP, Koren S, Phillippy AM, McVey DS, Kuszak J, Clawson ML, Harhay DM, Heaton MP, Chitko-McKown CG, Smith TP.

Genome Announc. 2013 May 16;1(3). pii: e00188-13. doi: 10.1128/genomeA.00188-13.

PMID:
23682137
[PubMed]
Free PMC Article
11.

Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis.

Harrington R, Ondov BD, Radune D, Friss MB, Klubnik J, Diviak L, Hnath J, Cendrowski SR, Blank TE, Karaolis D, Friedlander AM, Burans JP, Rosovitz MJ, Treangen T, Phillippy AM, Bergman NH.

Genome Announc. 2013 Jan;1(1). pii: e00067-12. doi: 10.1128/genomeA.00067-12. Epub 2013 Jan 15.

PMID:
23405332
[PubMed - as supplied by publisher]
Free PMC Article
12.

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M.

Genome Biol. 2013 Jan 15;14(1):R2. doi: 10.1186/gb-2013-14-1-r2.

PMID:
23320958
[PubMed - in process]
Free PMC Article
13.

Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone.

Treangen TJ, Phillippy AM.

Genome Biol. 2012 Dec 27;13(12):181. doi: 10.1186/gb-2012-13-12-181.

PMID:
23270611
[PubMed - in process]
Free PMC Article
14.

Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe.

Price EP, Seymour ML, Sarovich DS, Latham J, Wolken SR, Mason J, Vincent G, Drees KP, Beckstrom-Sternberg SM, Phillippy AM, Koren S, Okinaka RT, Chung WK, Schupp JM, Wagner DM, Vipond R, Foster JT, Bergman NH, Burans J, Pearson T, Brooks T, Keim P.

Emerg Infect Dis. 2012 Aug;18(8):1307-13. doi: 10.3201/eid1808.111343.

PMID:
22840345
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

The rise of a digital immune system.

Schatz MC, Phillippy AM.

Gigascience. 2012 Jul 12;1(1):4. doi: 10.1186/2047-217X-1-4.

PMID:
23587178
[PubMed]
Free PMC Article
16.

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.

Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M.

Brief Bioinform. 2013 Mar;14(2):213-24. doi: 10.1093/bib/bbr074. Epub 2011 Dec 23.

PMID:
22199379
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

GAGE: A critical evaluation of genome assemblies and assembly algorithms.

Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA.

Genome Res. 2012 Mar;22(3):557-67. doi: 10.1101/gr.131383.111. Epub 2012 Jan 6. Erratum in: Genome Res. 2012 Jun;22(6):1196.

PMID:
22147368
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis.

Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW.

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):E1423-32. doi: 10.1073/pnas.1111712108. Epub 2011 Nov 28.

PMID:
22123943
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Interactive metagenomic visualization in a Web browser.

Ondov BD, Bergman NH, Phillippy AM.

BMC Bioinformatics. 2011 Sep 30;12:385. doi: 10.1186/1471-2105-12-385.

PMID:
21961884
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.

Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.

PMID:
21926179
[PubMed - indexed for MEDLINE]
Free PMC Article
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