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A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist").
Brůna T, Aryal R, Dudchenko O, Sargent DJ, Mead D, Buti M, Cavallini A, Hytönen T, Andrés J, Pham M, Weisz D, Mascagni F, Usai G, Natali L, Bassil N, Fernandez GE, Lomsadze A, Armour M, Olukolu B, Poorten T, Britton C, Davik J, Ashrafi H, Aiden EL, Borodovsky M, Worthington M. Brůna T, et al. Among authors: borodovsky m. G3 (Bethesda). 2023 Feb 9;13(2):jkac289. doi: 10.1093/g3journal/jkac289. G3 (Bethesda). 2023. PMID: 36331334 Free PMC article.
Improving gene annotation of complete viral genomes.
Mills R, Rozanov M, Lomsadze A, Tatusova T, Borodovsky M. Mills R, et al. Among authors: borodovsky m. Nucleic Acids Res. 2003 Dec 1;31(23):7041-55. doi: 10.1093/nar/gkg878. Nucleic Acids Res. 2003. PMID: 14627837 Free PMC article.
Frameshift detection in prokaryotic genomic sequences.
Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M. Kislyuk A, et al. Among authors: borodovsky m. Int J Bioinform Res Appl. 2009;5(4):458-77. doi: 10.1504/IJBRA.2009.027519. Int J Bioinform Res Appl. 2009. PMID: 19640832
Ab initio gene identification in metagenomic sequences.
Zhu W, Lomsadze A, Borodovsky M. Zhu W, et al. Among authors: borodovsky m. Nucleic Acids Res. 2010 Jul;38(12):e132. doi: 10.1093/nar/gkq275. Epub 2010 Apr 19. Nucleic Acids Res. 2010. PMID: 20403810 Free PMC article.
The genome of woodland strawberry (Fragaria vesca).
Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM. Shulaev V, et al. Among authors: borodovsky m. Nat Genet. 2011 Feb;43(2):109-16. doi: 10.1038/ng.740. Epub 2010 Dec 26. Nat Genet. 2011. PMID: 21186353 Free PMC article.
Identification of protein coding regions in RNA transcripts.
Tang S, Lomsadze A, Borodovsky M. Tang S, et al. Among authors: borodovsky m. Nucleic Acids Res. 2015 Jul 13;43(12):e78. doi: 10.1093/nar/gkv227. Epub 2015 Apr 13. Nucleic Acids Res. 2015. PMID: 25870408 Free PMC article.
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