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Rapid and sensitive detection of genome contamination at scale with FCS-GX.
Astashyn A, Tvedte ES, Sweeney D, Sapojnikov V, Bouk N, Joukov V, Mozes E, Strope PK, Sylla PM, Wagner L, Bidwell SL, Clark K, Davis EW, Smith-White B, Hlavina W, Pruitt KD, Schneider VA, Murphy TD. Astashyn A, et al. Among authors: pruitt kd. bioRxiv [Preprint]. 2023 Jun 6:2023.06.02.543519. doi: 10.1101/2023.06.02.543519. bioRxiv. 2023. PMID: 37292984 Free PMC article. Updated. Preprint.
RefSeq: an update on mammalian reference sequences.
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, DiCuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. Pruitt KD, et al. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. doi: 10.1093/nar/gkt1114. Epub 2013 Nov 19. Nucleic Acids Res. 2014. PMID: 24259432 Free PMC article.
Gene: a gene-centered information resource at NCBI.
Brown GR, Hem V, Katz KS, Ovetsky M, Wallin C, Ermolaeva O, Tolstoy I, Tatusova T, Pruitt KD, Maglott DR, Murphy TD. Brown GR, et al. Among authors: pruitt kd. Nucleic Acids Res. 2015 Jan;43(Database issue):D36-42. doi: 10.1093/nar/gku1055. Epub 2014 Oct 29. Nucleic Acids Res. 2015. PMID: 25355515 Free PMC article.
Mouse genome annotation by the RefSeq project.
McGarvey KM, Goldfarb T, Cox E, Farrell CM, Gupta T, Joardar VS, Kodali VK, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Webb D, Wright MW, Murphy TD, Pruitt KD. McGarvey KM, et al. Among authors: pruitt kd. Mamm Genome. 2015 Oct;26(9-10):379-90. doi: 10.1007/s00335-015-9585-8. Epub 2015 Jul 28. Mamm Genome. 2015. PMID: 26215545 Free PMC article.
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.
O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD. O'Leary NA, et al. Among authors: pruitt kd. Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45. doi: 10.1093/nar/gkv1189. Epub 2015 Nov 8. Nucleic Acids Res. 2016. PMID: 26553804 Free PMC article.
Assembly: a resource for assembled genomes at NCBI.
Kitts PA, Church DM, Thibaud-Nissen F, Choi J, Hem V, Sapojnikov V, Smith RG, Tatusova T, Xiang C, Zherikov A, DiCuccio M, Murphy TD, Pruitt KD, Kimchi A. Kitts PA, et al. Among authors: pruitt kd. Nucleic Acids Res. 2016 Jan 4;44(D1):D73-80. doi: 10.1093/nar/gkv1226. Epub 2015 Nov 17. Nucleic Acids Res. 2016. PMID: 26578580 Free PMC article.
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure.
Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB, Cheng HH. Warren WC, et al. Among authors: pruitt kd. G3 (Bethesda). 2017 Jan 5;7(1):109-117. doi: 10.1534/g3.116.035923. G3 (Bethesda). 2017. PMID: 27852011 Free PMC article.
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Schneider VA, et al. Among authors: pruitt kd. Genome Res. 2017 May;27(5):849-864. doi: 10.1101/gr.213611.116. Epub 2017 Apr 10. Genome Res. 2017. PMID: 28396521 Free PMC article.
100 results