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Major data analysis errors invalidate cancer microbiome findings.
Gihawi A, Ge Y, Lu J, Puiu D, Xu A, Cooper CS, Brewer DS, Pertea M, Salzberg SL. Gihawi A, et al. Among authors: puiu d. mBio. 2023 Oct 31;14(5):e0160723. doi: 10.1128/mbio.01607-23. Epub 2023 Oct 9. mBio. 2023. PMID: 37811944 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.
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.
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.
The MaSuRCA genome assembler.
Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. Zimin AV, et al. Among authors: puiu d. Bioinformatics. 2013 Nov 1;29(21):2669-77. doi: 10.1093/bioinformatics/btt476. Epub 2013 Aug 29. Bioinformatics. 2013. PMID: 23990416 Free PMC article.
Insights into the loblolly pine genome: characterization of BAC and fosmid sequences.
Wegrzyn JL, Lin BY, Zieve JJ, Dougherty WM, Martínez-García PJ, Koriabine M, Holtz-Morris A, deJong P, Crepeau M, Langley CH, Puiu D, Salzberg SL, Neale DB, Stevens KA. Wegrzyn JL, et al. Among authors: puiu d. PLoS One. 2013 Sep 4;8(9):e72439. doi: 10.1371/journal.pone.0072439. eCollection 2013. PLoS One. 2013. PMID: 24023741 Free PMC article.
73 results