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Page 1
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. Salzberg SL, et al. Among authors: puiu d. Genome Res. 2012 Mar;22(3):557-67. doi: 10.1101/gr.131383.111. Epub 2012 Jan 6. Genome Res. 2012. PMID: 22147368 Free PMC article.
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.
Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, Aparna G, Jha G, Pandey A, Patil PB, Ishihara H, Meyer DF, Szurek B, Verdier V, Koebnik R, Dow JM, Ryan RP, Hirata H, Tsuyumu S, Won Lee S, Seo YS, Sriariyanum M, Ronald PC, Sonti RV, Van Sluys MA, Leach JE, White FF, Bogdanove AJ. Salzberg SL, et al. Among authors: puiu d. BMC Genomics. 2008 May 1;9:204. doi: 10.1186/1471-2164-9-204. BMC Genomics. 2008. PMID: 18452608 Free PMC article.
A whole-genome assembly of the domestic cow, Bos taurus.
Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL. Zimin AV, et al. Among authors: puiu d. Genome Biol. 2009;10(4):R42. doi: 10.1186/gb-2009-10-4-r42. Epub 2009 Apr 24. Genome Biol. 2009. PMID: 19393038 Free PMC article.
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM. Dalloul RA, et al. Among authors: puiu d. PLoS Biol. 2010 Sep 7;8(9):e1000475. doi: 10.1371/journal.pbio.1000475. PLoS Biol. 2010. PMID: 20838655 Free PMC article.
Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.
Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, Schatz MC, Shumway M, Sommer DD, Trapnell C, Benahmed F, Dimitrov G, Madupu R, Radune D, Sullivan S, Jha G, Ishihara H, Lee SW, Pandey A, Sharma V, Sriariyanun M, Szurek B, Vera-Cruz CM, Dorman KS, Ronald PC, Verdier V, Dow JM, Sonti RV, Tsuge S, Brendel VP, Rabinowicz PD, Leach JE, White FF, Salzberg SL. Bogdanove AJ, et al. Among authors: puiu d. J Bacteriol. 2011 Oct;193(19):5450-64. doi: 10.1128/JB.05262-11. Epub 2011 Jul 22. J Bacteriol. 2011. PMID: 21784931 Free PMC article.
GAGE-B: an evaluation of genome assemblers for bacterial organisms.
Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL. Magoc T, et al. Among authors: puiu d. Bioinformatics. 2013 Jul 15;29(14):1718-25. doi: 10.1093/bioinformatics/btt273. Epub 2013 May 10. Bioinformatics. 2013. PMID: 23665771 Free PMC article.
77 results