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Items: 1 to 20 of 80

1.

Filovirus RefSeq entries: evaluation and selection of filovirus type variants, type sequences, and names.

Kuhn JH, Andersen KG, Bào Y, Bavari S, Becker S, Bennett RS, Bergman NH, Blinkova O, Bradfute S, Brister JR, Bukreyev A, Chandran K, Chepurnov AA, Davey RA, Dietzgen RG, Doggett NA, Dolnik O, Dye JM, Enterlein S, Fenimore PW, Formenty P, Freiberg AN, Garry RF, Garza NL, Gire SK, Gonzalez JP, Griffiths A, Happi CT, Hensley LE, Herbert AS, Hevey MC, Hoenen T, Honko AN, Ignatyev GM, Jahrling PB, Johnson JC, Johnson KM, Kindrachuk J, Klenk HD, Kobinger G, Kochel TJ, Lackemeyer MG, Lackner DF, Leroy EM, Lever MS, Mühlberger E, Netesov SV, Olinger GG, Omilabu SA, Palacios G, Panchal RG, Park DJ, Patterson JL, Paweska JT, Peters CJ, Pettitt J, Pitt L, Radoshitzky SR, Ryabchikova EI, Saphire EO, Sabeti PC, Sealfon R, Shestopalov AM, Smither SJ, Sullivan NJ, Swanepoel R, Takada A, Towner JS, van der Groen G, Volchkov VE, Volchkova VA, Wahl-Jensen V, Warren TK, Warfield KL, Weidmann M, Nichol ST.

Viruses. 2014 Sep 26;6(9):3663-82. doi: 10.3390/v6093663.

2.

Virus nomenclature below the species level: a standardized nomenclature for filovirus strains and variants rescued from cDNA.

Kuhn JH, Bào Y, Bavari S, Becker S, Bradfute S, Brauburger K, Rodney Brister J, Bukreyev AA, Caì Y, Chandran K, Davey RA, Dolnik O, Dye JM, Enterlein S, Gonzalez JP, Formenty P, Freiberg AN, Hensley LE, Hoenen T, Honko AN, Ignatyev GM, Jahrling PB, Johnson KM, Klenk HD, Kobinger G, Lackemeyer MG, Leroy EM, Lever MS, Mühlberger E, Netesov SV, Olinger GG, Palacios G, Patterson JL, Paweska JT, Pitt L, Radoshitzky SR, Ryabchikova EI, Saphire EO, Shestopalov AM, Smither SJ, Sullivan NJ, Swanepoel R, Takada A, Towner JS, van der Groen G, Volchkov VE, Volchkova VA, Wahl-Jensen V, Warren TK, Warfield KL, Weidmann M, Nichol ST.

Arch Virol. 2014 May;159(5):1229-37. doi: 10.1007/s00705-013-1877-2. Epub 2013 Nov 5.

3.

Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses.

Bào Y, Amarasinghe GK, Basler CF, Bavari S, Bukreyev A, Chandran K, Dolnik O, Dye JM, Ebihara H, Formenty P, Hewson R, Kobinger GP, Leroy EM, Mühlberger E, Netesov SV, Patterson JL, Paweska JT, Smither SJ, Takada A, Towner JS, Volchkov VE, Wahl-Jensen V, Kuhn JH.

Viruses. 2017 May 11;9(5). pii: E106. doi: 10.3390/v9050106.

4.

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

Pruitt KD, Tatusova T, Maglott DR.

Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5. Epub 2006 Nov 27.

5.

Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution.

Brody T, Yavatkar AS, Park DS, Kuzin A, Ross J, Odenwald WF.

PLoS Negl Trop Dis. 2017 Jun 16;11(6):e0005673. doi: 10.1371/journal.pntd.0005673. eCollection 2017 Jun.

6.

PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses.

Bao Y, Chetvernin V, Tatusova T.

Viruses. 2012 Aug;4(8):1318-27. Epub 2012 Aug 20.

7.

Comparison of RefSeq protein-coding regions in human and vertebrate genomes.

Fong JH, Murphy TD, Pruitt KD.

BMC Genomics. 2013 Sep 25;14:654. doi: 10.1186/1471-2164-14-654.

8.

Filoviruses are ancient and integrated into mammalian genomes.

Taylor DJ, Leach RW, Bruenn J.

BMC Evol Biol. 2010 Jun 22;10:193. doi: 10.1186/1471-2148-10-193.

9.

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

Pruitt KD, Tatusova T, Maglott DR.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.

10.

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.

Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45. doi: 10.1093/nar/gkv1189. Epub 2015 Nov 8.

11.

RefSeq: an update on prokaryotic genome annotation and curation.

Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V, O'Neill K, Li W, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu F, Marchler GH, Song JS, Thanki N, Yamashita RA, Zheng C, Thibaud-Nissen F, Geer LY, Marchler-Bauer A, Pruitt KD.

Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860. doi: 10.1093/nar/gkx1068.

12.

Development and evaluation of a panel of filovirus sequence capture probes for pathogen detection by next-generation sequencing.

Koehler JW, Hall AT, Rolfe PA, Honko AN, Palacios GF, Fair JN, Muyembe JJ, Mulembekani P, Schoepp RJ, Adesokan A, Minogue TD.

PLoS One. 2014 Sep 10;9(9):e107007. doi: 10.1371/journal.pone.0107007. eCollection 2014.

13.

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.

Mamm Genome. 2015 Oct;26(9-10):379-90. doi: 10.1007/s00335-015-9585-8. Epub 2015 Jul 28.

14.

Rapid molecular strategy for filovirus detection and characterization.

Zhai J, Palacios G, Towner JS, Jabado O, Kapoor V, Venter M, Grolla A, Briese T, Paweska J, Swanepoel R, Feldmann H, Nichol ST, Lipkin WI.

J Clin Microbiol. 2007 Jan;45(1):224-6. Epub 2006 Nov 1.

15.

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.

Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. doi: 10.1093/nar/gkt1114. Epub 2013 Nov 19.

16.

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy.

Pruitt KD, Tatusova T, Brown GR, Maglott DR.

Nucleic Acids Res. 2012 Jan;40(Database issue):D130-5. doi: 10.1093/nar/gkr1079. Epub 2011 Nov 24.

17.

Evolutionary maintenance of filovirus-like genes in bat genomes.

Taylor DJ, Dittmar K, Ballinger MJ, Bruenn JA.

BMC Evol Biol. 2011 Nov 17;11:336. doi: 10.1186/1471-2148-11-336.

18.

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.

Nucleic Acids Res. 2015 Jan;43(Database issue):D36-42. doi: 10.1093/nar/gku1055. Epub 2014 Oct 29.

19.

Genetics-based classification of filoviruses calls for expanded sampling of genomic sequences.

Lauber C, Gorbalenya AE.

Viruses. 2012 Sep;4(9):1425-37. doi: 10.3390/v4091425. Epub 2012 Aug 31.

20.

Current perspectives on the phylogeny of Filoviridae.

Barrette RW, Xu L, Rowland JM, McIntosh MT.

Infect Genet Evol. 2011 Oct;11(7):1514-9. doi: 10.1016/j.meegid.2011.06.017. Epub 2011 Jun 30. Review.

PMID:
21742058

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