Stadler T - Search Results

1

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, Kühnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C; PANGEA-HIV Consortium. Ratmann O, et al. Among authors: stadler t. Mol Biol Evol. 2017 Jan;34(1):185-203. doi: 10.1093/molbev/msw217. Epub 2016 Oct 7. Mol Biol Evol. 2017. PMID: 28053012 Free PMC article.

2

Estimating the basic reproductive number from viral sequence data.

Stadler T, Kouyos R, von Wyl V, Yerly S, Böni J, Bürgisser P, Klimkait T, Joos B, Rieder P, Xie D, Günthard HF, Drummond AJ, Bonhoeffer S; Swiss HIV Cohort Study. Stadler T, et al. Mol Biol Evol. 2012 Jan;29(1):347-57. doi: 10.1093/molbev/msr217. Epub 2011 Sep 2. Mol Biol Evol. 2012. PMID: 21890480

3

Inferring epidemic contact structure from phylogenetic trees.

Leventhal GE, Kouyos R, Stadler T, Wyl Vv, Yerly S, Böni J, Cellerai C, Klimkait T, Günthard HF, Bonhoeffer S. Leventhal GE, et al. Among authors: stadler t. PLoS Comput Biol. 2012;8(3):e1002413. doi: 10.1371/journal.pcbi.1002413. Epub 2012 Mar 8. PLoS Comput Biol. 2012. PMID: 22412361 Free PMC article.

4

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV).

Stadler T, Kühnert D, Bonhoeffer S, Drummond AJ. Stadler T, et al. Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):228-33. doi: 10.1073/pnas.1207965110. Epub 2012 Dec 17. Proc Natl Acad Sci U S A. 2013. PMID: 23248286 Free PMC article.

5

Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission.

Leventhal GE, Günthard HF, Bonhoeffer S, Stadler T. Leventhal GE, et al. Among authors: stadler t. Mol Biol Evol. 2014 Jan;31(1):6-17. doi: 10.1093/molbev/mst172. Epub 2013 Oct 1. Mol Biol Evol. 2014. PMID: 24085839 Free PMC article.

6

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. Kühnert D, et al. Among authors: stadler t. J R Soc Interface. 2014 Feb 26;11(94):20131106. doi: 10.1098/rsif.2013.1106. Print 2014 May 6. J R Soc Interface. 2014. PMID: 24573331 Free PMC article.

7

Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics.

Lambert A, Alexander HK, Stadler T. Lambert A, et al. Among authors: stadler t. J Theor Biol. 2014 Jul 7;352:60-70. doi: 10.1016/j.jtbi.2014.02.031. Epub 2014 Mar 4. J Theor Biol. 2014. PMID: 24607743

8

Insights into the early epidemic spread of ebola in sierra leone provided by viral sequence data.

Stadler T, Kühnert D, Rasmussen DA, du Plessis L. Stadler T, et al. PLoS Curr. 2014 Oct 6;6:ecurrents.outbreaks.02bc6d927ecee7bbd33532ec8ba6a25f. doi: 10.1371/currents.outbreaks.02bc6d927ecee7bbd33532ec8ba6a25f. PLoS Curr. 2014. PMID: 25642370 Free PMC article.

9

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. Stadler T, et al. Proc Biol Sci. 2015 May 7;282(1806):20150420. doi: 10.1098/rspb.2015.0420. Proc Biol Sci. 2015. PMID: 25876846 Free PMC article.

10

Assessment of Overlap of Phylogenetic Transmission Clusters and Communities in Simple Sexual Contact Networks: Applications to HIV-1.

Villandre L, Stephens DA, Labbe A, Günthard HF, Kouyos R, Stadler T; Swiss HIV Cohort Study. Villandre L, et al. Among authors: stadler t. PLoS One. 2016 Feb 10;11(2):e0148459. doi: 10.1371/journal.pone.0148459. eCollection 2016. PLoS One. 2016. PMID: 26863322 Free PMC article.

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