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Items: 1 to 20 of 98

1.

Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales.

Low SJ, Džunková M, Chaumeil PA, Parks DH, Hugenholtz P.

Nat Microbiol. 2019 Aug;4(8):1306-1315. doi: 10.1038/s41564-019-0448-z. Epub 2019 May 20.

PMID:
31110365
2.

Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria.

Krupovic M, Forterre P, Bamford DH.

J Mol Biol. 2010 Mar 19;397(1):144-60. doi: 10.1016/j.jmb.2010.01.037. Epub 2010 Jan 25.

PMID:
20109464
3.

Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages.

Barylski J, Enault F, Dutilh BE, Schuller MB, Edwards RA, Gillis A, Klumpp J, Knezevic P, Krupovic M, Kuhn JH, Lavigne R, Oksanen HM, Sullivan MB, Jang HB, Simmonds P, Aiewsakun P, Wittmann J, Tolstoy I, Brister JR, Kropinski AM, Adriaenssens EM.

Syst Biol. 2020 Jan 1;69(1):110-123. doi: 10.1093/sysbio/syz036.

PMID:
31127947
4.

Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towards a unified taxonomy.

Aiewsakun P, Adriaenssens EM, Lavigne R, Kropinski AM, Simmonds P.

J Gen Virol. 2018 Sep;99(9):1331-1343. doi: 10.1099/jgv.0.001110. Epub 2018 Jul 17.

5.

Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny.

Bapteste E, Susko E, Leigh J, Ruiz-Trillo I, Bucknam J, Doolittle WF.

Mol Biol Evol. 2008 Jan;25(1):83-91. Epub 2007 Oct 16.

PMID:
17940208
6.
7.

A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria.

Kauffman KM, Hussain FA, Yang J, Arevalo P, Brown JM, Chang WK, VanInsberghe D, Elsherbini J, Sharma RS, Cutler MB, Kelly L, Polz MF.

Nature. 2018 Feb 1;554(7690):118-122. doi: 10.1038/nature25474. Epub 2018 Jan 24.

PMID:
29364876
8.

Concatenated alignments and the case of the disappearing tree.

Thiergart T, Landan G, Martin WF.

BMC Evol Biol. 2014 Dec 30;14:266. doi: 10.1186/s12862-014-0266-0.

9.

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria.

Bolduc B, Jang HB, Doulcier G, You ZQ, Roux S, Sullivan MB.

PeerJ. 2017 May 3;5:e3243. doi: 10.7717/peerj.3243. eCollection 2017.

10.

Tailed bacteriophages: the order caudovirales.

Ackermann HW.

Adv Virus Res. 1998;51:135-201. Review.

PMID:
9891587
11.

Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils.

Han LL, Yu DT, Zhang LM, Shen JP, He JZ.

Sci Rep. 2017 Mar 22;7:45142. doi: 10.1038/srep45142.

12.

Multilocus phylogeny of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota): insights on diversity, distributions, and a comparison of species tree and concatenated topologies.

Leavitt SD, Esslinger TL, Spribille T, Divakar PK, Thorsten Lumbsch H.

Mol Phylogenet Evol. 2013 Jan;66(1):138-52. doi: 10.1016/j.ympev.2012.09.013. Epub 2012 Sep 24.

PMID:
23017822
13.

Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.

Lang JM, Darling AE, Eisen JA.

PLoS One. 2013 Apr 25;8(4):e62510. doi: 10.1371/journal.pone.0062510. Print 2013.

14.

ICTV Virus Taxonomy Profile: Bicaudaviridae.

Prangishvili D, Krupovic M, Ictv Report Consortium.

J Gen Virol. 2018 Jul;99(7):864-865. doi: 10.1099/jgv.0.001106. Epub 2018 Jun 7.

PMID:
29877786
15.

Virus classification - where do you draw the line?

Simmonds P, Aiewsakun P.

Arch Virol. 2018 Aug;163(8):2037-2046. doi: 10.1007/s00705-018-3938-z. Epub 2018 Jul 24. Review.

16.

Evolution of the Large Nucleocytoplasmic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism.

Koonin EV, Yutin N.

Adv Virus Res. 2019;103:167-202. doi: 10.1016/bs.aivir.2018.09.002. Epub 2018 Nov 10. Review.

PMID:
30635076
17.

Defining bacterial species in the genomic era: insights from the genus Acinetobacter.

Chan JZ, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ.

BMC Microbiol. 2012 Dec 23;12:302. doi: 10.1186/1471-2180-12-302.

20.

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks.

Bin Jang H, Bolduc B, Zablocki O, Kuhn JH, Roux S, Adriaenssens EM, Brister JR, Kropinski AM, Krupovic M, Lavigne R, Turner D, Sullivan MB.

Nat Biotechnol. 2019 Jun;37(6):632-639. doi: 10.1038/s41587-019-0100-8. Epub 2019 May 6.

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