Holmes EC - Search Results

1

PHYRN: a robust method for phylogenetic analysis of highly divergent sequences.

Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, Chintapalli SV, Kline LA, Gotlin M, Hartranft DN, Patterson ME, Dave F, Smith EJ, Holmes EC, Patterson RL, van Rossum DB. Bhardwaj G, et al. Among authors: holmes ec. PLoS One. 2012;7(4):e34261. doi: 10.1371/journal.pone.0034261. Epub 2012 Apr 13. PLoS One. 2012. PMID: 22514627 Free PMC article.

2

Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity.

Chang GS, Hong Y, Ko KD, Bhardwaj G, Holmes EC, Patterson RL, van Rossum DB. Chang GS, et al. Among authors: holmes ec. Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13474-9. doi: 10.1073/pnas.0803860105. Epub 2008 Sep 2. Proc Natl Acad Sci U S A. 2008. PMID: 18765810 Free PMC article.

3

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. Shapiro B, et al. Among authors: holmes ec. Mol Biol Evol. 2006 Sep;23(9):1724-30. doi: 10.1093/molbev/msl037. Epub 2006 Jun 14. Mol Biol Evol. 2006. PMID: 16774976 Free article.

4

Discovering the phylodynamics of RNA viruses.

Holmes EC, Grenfell BT. Holmes EC, et al. PLoS Comput Biol. 2009 Oct;5(10):e1000505. doi: 10.1371/journal.pcbi.1000505. Epub 2009 Oct 26. PLoS Comput Biol. 2009. PMID: 19855824 Free PMC article. Review. No abstract available.

5

Phylogenetic analysis reveals rapid evolutionary dynamics in the plant RNA virus genus tobamovirus.

Pagán I, Firth C, Holmes EC. Pagán I, et al. Among authors: holmes ec. J Mol Evol. 2010 Oct;71(4):298-307. doi: 10.1007/s00239-010-9385-4. Epub 2010 Sep 14. J Mol Evol. 2010. PMID: 20838783

6

Family level phylogenies reveal modes of macroevolution in RNA viruses.

Kitchen A, Shackelton LA, Holmes EC. Kitchen A, et al. Among authors: holmes ec. Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):238-43. doi: 10.1073/pnas.1011090108. Epub 2010 Dec 20. Proc Natl Acad Sci U S A. 2011. PMID: 21173251 Free PMC article.

7

What does virus evolution tell us about virus origins?

Holmes EC. Holmes EC. J Virol. 2011 Jun;85(11):5247-51. doi: 10.1128/JVI.02203-10. Epub 2011 Mar 30. J Virol. 2011. PMID: 21450811 Free PMC article. Review.

8

Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses.

Holmes EC, Ghedin E, Miller N, Taylor J, Bao Y, St George K, Grenfell BT, Salzberg SL, Fraser CM, Lipman DJ, Taubenberger JK. Holmes EC, et al. PLoS Biol. 2005 Sep;3(9):e300. doi: 10.1371/journal.pbio.0030300. Epub 2005 Jul 26. PLoS Biol. 2005. PMID: 16026181 Free PMC article.

9

JC virus evolution and its association with human populations.

Shackelton LA, Rambaut A, Pybus OG, Holmes EC. Shackelton LA, et al. Among authors: holmes ec. J Virol. 2006 Oct;80(20):9928-33. doi: 10.1128/JVI.00441-06. J Virol. 2006. PMID: 17005670 Free PMC article.

10

Stochastic processes are key determinants of short-term evolution in influenza a virus.

Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, George KS, Griesemer SB, Ghedin E, Sengamalay NA, Spiro DJ, Volkov I, Grenfell BT, Lipman DJ, Taubenberger JK, Holmes EC. Nelson MI, et al. Among authors: holmes ec. PLoS Pathog. 2006 Dec;2(12):e125. doi: 10.1371/journal.ppat.0020125. PLoS Pathog. 2006. PMID: 17140286 Free PMC article.

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