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Items: 1 to 20 of 83

1.

Detecting natural selection in RNA virus populations using sequence summary statistics.

Bhatt S, Katzourakis A, Pybus OG.

Infect Genet Evol. 2010 Apr;10(3):421-30. doi: 10.1016/j.meegid.2009.06.001. Epub 2009 Jun 11.

PMID:
19524068
2.

A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution.

Shapiro B, Rambaut A, Pybus OG, Holmes EC.

Mol Biol Evol. 2006 Sep;23(9):1724-30. Epub 2006 Jun 14.

PMID:
16774976
3.

Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences.

Koonin EV, Dolja VV.

Crit Rev Biochem Mol Biol. 1993;28(5):375-430. Review. Erratum in: Crit Rev Biochem Mol Biol 1993;28(6):546.

PMID:
8269709
4.

A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses.

Fares MA, Elena SF, Ortiz J, Moya A, Barrio E.

J Mol Evol. 2002 Nov;55(5):509-21.

PMID:
12399925
5.

Evolution of mutational robustness in an RNA virus.

Montville R, Froissart R, Remold SK, Tenaillon O, Turner PE.

PLoS Biol. 2005 Nov;3(11):e381. Epub 2005 Nov 1.

6.

Genetic variation of populations of Citrus psorosis virus.

Martín S, García ML, Troisi A, Rubio L, Legarreta G, Grau O, Alioto D, Moreno P, Guerri J.

J Gen Virol. 2006 Oct;87(Pt 10):3097-102.

PMID:
16963769
7.

A phylogenetic survey of recombination frequency in plant RNA viruses.

Chare ER, Holmes EC.

Arch Virol. 2006 May;151(5):933-46. Epub 2005 Nov 15.

PMID:
16292597
8.

Homologous recombination in bovine pestiviruses. Phylogenetic and statistic evidence.

Jones LR, Weber EL.

Infect Genet Evol. 2004 Dec;4(4):335-43.

PMID:
15374531
9.

Automatic detection of conserved base pairing patterns in RNA virus genomes.

Hofacker IL, Stadler PF.

Comput Chem. 1999 Jun 15;23(3-4):401-14.

PMID:
10404627
10.

Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis.

Jenkins GM, Rambaut A, Pybus OG, Holmes EC.

J Mol Evol. 2002 Feb;54(2):156-65.

PMID:
11821909
11.

Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution.

Pybus OG, Rambaut A, Belshaw R, Freckleton RP, Drummond AJ, Holmes EC.

Mol Biol Evol. 2007 Mar;24(3):845-52. Epub 2007 Jan 11.

PMID:
17218639
12.

New genera of RNA viruses in subtropical seawater, inferred from polymerase gene sequences.

Culley AI, Steward GF.

Appl Environ Microbiol. 2007 Sep;73(18):5937-44. Epub 2007 Jul 20.

13.

Automatic detection of conserved RNA structure elements in complete RNA virus genomes.

Hofacker IL, Fekete M, Flamm C, Huynen MA, Rauscher S, Stolorz PE, Stadler PF.

Nucleic Acids Res. 1998 Aug 15;26(16):3825-36.

14.

Composition bias and genome polarity of RNA viruses.

Auewarakul P.

Virus Res. 2005 Apr;109(1):33-7. Epub 2004 Nov 18.

PMID:
15826910
15.

A comparison of the nucleotide sequences of eastern and western equine encephalomyelitis viruses with those of other alphaviruses and related RNA viruses.

Weaver SC, Hagenbaugh A, Bellew LA, Netesov SV, Volchkov VE, Chang GJ, Clarke DK, Gousset L, Scott TW, Trent DW, et al.

Virology. 1993 Nov;197(1):375-90. Erratum in: Virology. 1994 Aug 1;202(2):1083.

PMID:
8105605
16.

Adaptation of a diverse simian immunodeficiency virus population to a new host is revealed through a systematic approach to identify amino acid sites under selection.

Vanderford TH, Demma LJ, Feinberg MB, Staprans SI, Logsdon JM Jr.

Mol Biol Evol. 2007 Mar;24(3):660-9. Epub 2006 Dec 11.

PMID:
17159231
17.
18.

Metagenomic analysis of coastal RNA virus communities.

Culley AI, Lang AS, Suttle CA.

Science. 2006 Jun 23;312(5781):1795-8.

19.

Complete nucleotide sequences and genome characterization of a novel double-stranded RNA virus infecting Rosa multiflora.

Salem NM, Golino DA, Falk BW, Rowhani A.

Arch Virol. 2008;153(3):455-62. doi: 10.1007/s00705-007-0008-3. Epub 2008 Jan 3.

PMID:
18172568
20.

Not so different after all: a comparison of methods for detecting amino acid sites under selection.

Kosakovsky Pond SL, Frost SD.

Mol Biol Evol. 2005 May;22(5):1208-22. Epub 2005 Feb 9.

PMID:
15703242

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