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Items: 16

1.

Detection of HIV transmission clusters from phylogenetic trees using a multi-state birth-death model.

Barido-Sottani J, Vaughan TG, Stadler T.

J R Soc Interface. 2018 Sep;15(146). pii: 20180512. doi: 10.1098/rsif.2018.0512.

2.

Taming the BEAST-A Community Teaching Material Resource for BEAST 2.

Barido-Sottani J, Bošková V, Plessis LD, Kühnert D, Magnus C, Mitov V, Müller NF, PecErska J, Rasmussen DA, Zhang C, Drummond AJ, Heath TA, Pybus OG, Vaughan TG, Stadler T.

Syst Biol. 2018 Jan 1;67(1):170-174. doi: 10.1093/sysbio/syx060.

3.

IcyTree: rapid browser-based visualization for phylogenetic trees and networks.

Vaughan TG.

Bioinformatics. 2017 Aug 1;33(15):2392-2394. doi: 10.1093/bioinformatics/btx155.

4.

Inferring Ancestral Recombination Graphs from Bacterial Genomic Data.

Vaughan TG, Welch D, Drummond AJ, Biggs PJ, George T, French NP.

Genetics. 2017 Feb;205(2):857-870. doi: 10.1534/genetics.116.193425. Epub 2016 Dec 22.

5.

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.

Kühnert D, Stadler T, Vaughan TG, Drummond AJ.

Mol Biol Evol. 2016 Aug;33(8):2102-16. doi: 10.1093/molbev/msw064. Epub 2016 Apr 9.

6.

Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial.

Pacioni C, Hunt H, Allentoft ME, Vaughan TG, Wayne AF, Baynes A, Haouchar D, Dortch J, Bunce M.

Mol Ecol. 2015 Dec;24(23):5813-28. doi: 10.1111/mec.13430. Epub 2015 Nov 24.

PMID:
26497007
7.

Molecular Approaches to Understanding Transmission and Source Attribution in Nontyphoidal Salmonella and Their Application in Africa.

Mather AE, Vaughan TG, French NP.

Clin Infect Dis. 2015 Nov 1;61 Suppl 4:S259-65. doi: 10.1093/cid/civ727. Review.

PMID:
26449940
8.

How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?

Stadler T, Vaughan TG, Gavryushkin A, Guindon S, Kühnert D, Leventhal GE, Drummond AJ.

Proc Biol Sci. 2015 May 7;282(1806):20150420. doi: 10.1098/rspb.2015.0420.

9.

Efficient Bayesian inference under the structured coalescent.

Vaughan TG, Kühnert D, Popinga A, Welch D, Drummond AJ.

Bioinformatics. 2014 Aug 15;30(16):2272-9. doi: 10.1093/bioinformatics/btu201. Epub 2014 Apr 20.

10.

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model.

Kühnert D, Stadler T, Vaughan TG, Drummond AJ.

J R Soc Interface. 2014 Feb 26;11(94):20131106. doi: 10.1098/rsif.2013.1106. Print 2014 May 6.

11.

A stochastic simulator of birth-death master equations with application to phylodynamics.

Vaughan TG, Drummond AJ.

Mol Biol Evol. 2013 Jun;30(6):1480-93. doi: 10.1093/molbev/mst057. Epub 2013 Mar 16.

12.

Within-host demographic fluctuations and correlations in early retroviral infection.

Vaughan TG, Drummond PD, Drummond AJ.

J Theor Biol. 2012 Feb 21;295:86-99. doi: 10.1016/j.jtbi.2011.11.016. Epub 2011 Nov 25.

PMID:
22133472
13.

An α-diaminoboryl carbanion assisted stereoselective single-pot preparation of α,β-disubstituted acrylonitriles.

Tomioka T, Sankranti R, Vaughan TG, Maejima T, Yanase T.

J Org Chem. 2011 Oct 7;76(19):8053-8. doi: 10.1021/jo201280x. Epub 2011 Aug 29.

PMID:
21870881
14.

Einstein-Podolsky-Rosen entanglement strategies in two-well Bose-Einstein condensates.

He QY, Reid MD, Vaughan TG, Gross C, Oberthaler M, Drummond PD.

Phys Rev Lett. 2011 Mar 25;106(12):120405. Epub 2011 Mar 23.

PMID:
21517288
15.

Extinction times in autocatalytic systems.

Drummond PD, Vaughan TG, Drummond AJ.

J Phys Chem A. 2010 Oct 7;114(39):10481-91. doi: 10.1021/jp104471e.

PMID:
20831232
16.

A facile, one-pot synthesis of beta-substituted (Z)-acrylonitriles utilizing an alpha-diaminoboryl carbanion.

Tomioka T, Takahashi Y, Vaughan TG, Yanase T.

Org Lett. 2010 May 21;12(10):2171-3. doi: 10.1021/ol100534s.

PMID:
20426398

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