Kosakovsky Pond SL - Search Results

1

Phylodynamics of infectious disease epidemics.

Volz EM, Kosakovsky Pond SL, Ward MJ, Leigh Brown AJ, Frost SD. Volz EM, et al. Among authors: kosakovsky pond sl. Genetics. 2009 Dec;183(4):1421-30. doi: 10.1534/genetics.109.106021. Epub 2009 Sep 21. Genetics. 2009. PMID: 19797047 Free PMC article.

2

An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1.

Kosakovsky Pond SL, Posada D, Stawiski E, Chappey C, Poon AF, Hughes G, Fearnhill E, Gravenor MB, Leigh Brown AJ, Frost SD. Kosakovsky Pond SL, et al. PLoS Comput Biol. 2009 Nov;5(11):e1000581. doi: 10.1371/journal.pcbi.1000581. Epub 2009 Nov 26. PLoS Comput Biol. 2009. PMID: 19956739 Free PMC article.

3

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

Kosakovsky Pond SL, Frost SD. Kosakovsky Pond SL, et al. Mol Biol Evol. 2005 May;22(5):1208-22. doi: 10.1093/molbev/msi105. Epub 2005 Feb 9. Mol Biol Evol. 2005. PMID: 15703242

4

Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus.

Poon AF, Kosakovsky Pond SL, Bennett P, Richman DD, Leigh Brown AJ, Frost SD. Poon AF, et al. Among authors: kosakovsky pond sl. PLoS Pathog. 2007 Mar;3(3):e45. doi: 10.1371/journal.ppat.0030045. PLoS Pathog. 2007. PMID: 17397261 Free PMC article.

5

The global transmission network of HIV-1.

Wertheim JO, Leigh Brown AJ, Hepler NL, Mehta SR, Richman DD, Smith DM, Kosakovsky Pond SL. Wertheim JO, et al. Among authors: kosakovsky pond sl. J Infect Dis. 2014 Jan 15;209(2):304-13. doi: 10.1093/infdis/jit524. Epub 2013 Oct 22. J Infect Dis. 2014. PMID: 24151309 Free PMC article.

6

HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens.

Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. Kosakovsky Pond SL, et al. Mol Biol Evol. 2018 Jul 1;35(7):1812-1819. doi: 10.1093/molbev/msy016. Mol Biol Evol. 2018. PMID: 29401317 Free PMC article.

7

Estimating selection pressures on HIV-1 using phylogenetic likelihood models.

Kosakovsky Pond SL, Poon AF, Zárate S, Smith DM, Little SJ, Pillai SK, Ellis RJ, Wong JK, Leigh Brown AJ, Richman DD, Frost SD. Kosakovsky Pond SL, et al. Stat Med. 2008 Oct 15;27(23):4779-89. doi: 10.1002/sim.3192. Stat Med. 2008. PMID: 18381707 Free PMC article.

8

Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients.

Poon AF, Kosakovsky Pond SL, Richman DD, Frost SD. Poon AF, et al. Among authors: kosakovsky pond sl. J Virol. 2007 Dec;81(24):13598-607. doi: 10.1128/JVI.01570-07. Epub 2007 Oct 3. J Virol. 2007. PMID: 17913806 Free PMC article.

9

A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus.

Kosakovsky Pond SL, Poon AF, Leigh Brown AJ, Frost SD. Kosakovsky Pond SL, et al. Mol Biol Evol. 2008 Sep;25(9):1809-24. doi: 10.1093/molbev/msn123. Epub 2008 May 29. Mol Biol Evol. 2008. PMID: 18511426 Free PMC article.

10

Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.

Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD. Poon AF, et al. Among authors: kosakovsky pond sl. Mol Biol Evol. 2010 Apr;27(4):819-32. doi: 10.1093/molbev/msp289. Epub 2009 Dec 2. Mol Biol Evol. 2010. PMID: 19955476 Free PMC article.

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