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1

Ancient DNA: Would the Real Neandertal Please Stand up?

Alan Cooper, Alexei J. Drummond, Eske Willerslev

Journal:

Current Biology

Year:

2004

Language:

english

File:

PDF, 67 KB

english, 2004

2

Bayesian Evolutionary Analysis with BEAST || Getting started with BEAST 2

Drummond, Alexei J., Bouckaert, Remco R.

Year:

2015

Language:

english

File:

PDF, 2.16 MB

english, 2015

3

Bayesian Evolutionary Analysis with BEAST || Putting it all together

Drummond, Alexei J., Bouckaert, Remco R.

Year:

2015

Language:

english

File:

PDF, 334 KB

english, 2015

4

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Suchard, Marc A, Lemey, Philippe, Baele, Guy, Ayres, Daniel L, Drummond, Alexei J, Rambaut, Andrew

Journal:

Virus Evolution

Year:

2018

Language:

english

File:

PDF, 5.29 MB

english, 2018

5

BEAST: Bayesian evolutionary analysis by sampling trees

Alexei J Drummond, Andrew Rambaut

Journal:

BMC Evolutionary Biology

Year:

2007

Language:

english

File:

PDF, 433 KB

english, 2007

6

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

Bouckaert, Remco, Heled, Joseph, Kühnert, Denise, Vaughan, Tim, Wu, Chieh-Hsi, Xie, Dong, Suchard, Marc A., Rambaut, Andrew, Drummond, Alexei J., Prlic, Andreas

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 707 KB

english, 2014

7

Bayesian phylogenetic estimation of fossil ages

Drummond, Alexei J., Stadler, Tanja

Journal:

Philosophical Transactions Biological Sciences

Year:

2016

Language:

english

File:

PDF, 2.19 MB

english, 2016

8

Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins

Gavryushkina, Alexandra, Heath, Tracy A., Ksepka, Daniel T., Stadler, Tanja, Welch, David, Drummond, Alexei J.

Journal:

Systematic Biology

Year:

2016

Language:

english

File:

PDF, 6.12 MB

english, 2016

9

Bayesian Evolutionary Analysis with BEAST || Bayesian evolutionary analysis by sampling trees

Drummond, Alexei J., Bouckaert, Remco R.

Year:

2015

Language:

english

File:

PDF, 7.56 MB

english, 2015

10

Bayesian Evolutionary Analysis with BEAST || Structured trees and phylogeography

Drummond, Alexei J., Bouckaert, Remco R.

Year:

2015

Language:

english

File:

PDF, 237 KB

english, 2015

11

Bayesian Evolutionary Analysis with BEAST || BEAST XML

Drummond, Alexei J., Bouckaert, Remco R.

Year:

2015

Language:

english

File:

PDF, 789 KB

english, 2015

12

Bayesian Evolutionary Analysis with BEAST || Exploring phylogenetic tree space

Drummond, Alexei J., Bouckaert, Remco R.

Year:

2015

Language:

english

File:

PDF, 9.34 MB

english, 2015

13

Bayesian Evolutionary Analysis with BEAST || References

Drummond, Alexei J., Bouckaert, Remco R.

Year:

2015

Language:

english

File:

PDF, 254 KB

english, 2015

14

Bayesian Evolutionary Analysis with BEAST || Coding and design patterns

Drummond, Alexei J., Bouckaert, Remco R.

Year:

2015

Language:

english

File:

PDF, 201 KB

english, 2015

15

Bayesian Evolutionary Analysis with BEAST || Advanced analysis

Drummond, Alexei J., Bouckaert, Remco R.

Year:

2015

Language:

english

File:

PDF, 2.27 MB

english, 2015

16

Bayesian Evolutionary Analysis with BEAST || Posterior analysis and post-processing

Drummond, Alexei J., Bouckaert, Remco R.

Year:

2015

Language:

english

File:

PDF, 724 KB

english, 2015

17

Bayesian Evolutionary Analysis with BEAST || Preface

Drummond, Alexei J., Bouckaert, Remco R.

Year:

2015

Language:

english

File:

PDF, 46 KB

english, 2015

18

The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes

Stadler, Tanja, Gavryushkina, Alexandra, Warnock, Rachel C.M., Drummond, Alexei J., Heath, Tracy A.

Journal:

Journal of Theoretical Biology

Year:

2018

Language:

english

File:

PDF, 2.52 MB

english, 2018

19

Bayesian inference and comparison of stochastic transcription elongation models

Douglas, Jordan, Kingston, Richard, Drummond, Alexei J., Hatzimanikatis, Vassily

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.67 MB

2020

20

Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework

Jan Strugnell, Mark Norman, Jennifer Jackson, Alexei J. Drummond, Alan Cooper

Journal:

Molecular Phylogenetics and Evolution

Year:

2005

Language:

english

File:

PDF, 550 KB

english, 2005

21

Tree measures and the number of segregating sites in time-structured population samples

Roald Forsberg, Alexei J Drummond, Jotun Hein

Journal:

Year:

2005

Language:

english

File:

PDF, 766 KB

english, 2005

22

Fully Bayesian tests of neutrality using genealogical summary statistics

Alexei J Drummond, Marc A Suchard

Journal:

Year:

2008

Language:

english

File:

PDF, 432 KB

english, 2008

23

Bayesian random local clocks, or one rate to rule them all

Alexei J Drummond, Marc A Suchard

Journal:

Year:

2010

Language:

english

File:

PDF, 829 KB

english, 2010

24

Divergence time estimates for major cephalopod groups: evidence from multiple genes

Jan Strugnell, Jennifer Jackson, Alexei J. Drummond, Alan Cooper

Journal:

Year:

2006

Language:

english

File:

PDF, 193 KB

english, 2006

25

Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis

Bunce, Michael, Worthy, Trevor H., Ford, Tom, Hoppitt, Will, Willerslev, Eske, Drummond, Alexei, Cooper, Alan

Journal:

Year:

2003

Language:

english

File:

PDF, 438 KB

english, 2003

26

Neotenous origins for pelagic octopuses

Jan Strugnell, Mark Norman, Alexei J Drummond, Alan Cooper

Journal:

Current Biology

Year:

2004

Language:

english

File:

PDF, 1.34 MB

english, 2004

27

Phylogenetic and epidemic modeling of rapidly evolving infectious diseases

Denise Kühnert, Chieh-Hsi Wu, Alexei J. Drummond

Journal:

Infection, Genetics and Evolution

Year:

2011

Language:

english

File:

PDF, 635 KB

english, 2011

28

Bayesian coestimation of phylogeny and sequence alignment

Gerton Lunter, István Miklós, Alexei Drummond, Ledet Jens Jensen, Jotun Hein

Journal:

BMC Bioinformatics

Year:

2005

Language:

english

File:

PDF, 354 KB

english, 2005

29

Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1

Charles TT Edwards, Edward C Holmes, Daniel J Wilson, Raphael P Viscidi, Elaine J Abrams, Rodney E Phillips, Alexei J Drummond

Journal:

BMC Evolutionary Biology

Year:

2006

Language:

english

File:

PDF, 375 KB

english, 2006

30

Bayesian inference of population size history from multiple loci

Joseph Heled, Alexei J Drummond

Journal:

BMC Evolutionary Biology

Year:

2008

Language:

english

File:

PDF, 1.20 MB

english, 2008

31

Evidence for Time Dependency of Molecular Rate Estimates

Simon Y. W. Ho, Beth Shapiro, Matthew J. Phillips, Alan Cooper and Alexei J. Drummond

Journal:

Systematic Biology

Year:

2007

Language:

english

File:

PDF, 1.56 MB

english, 2007

32

Measurably evolving populations

Alexei J. Drummond, Oliver G. Pybus, Andrew Rambaut, Roald Forsberg, Allen G. Rodrigo

Journal:

Trends in Ecology & Evolution

Year:

2003

Language:

english

File:

PDF, 847 KB

english, 2003

33

Extinction Times in Autocatalytic Systems

Drummond, Peter D., Vaughan, Timothy G., Drummond, Alexei J.

Journal:

Journal of Physical Chemistry A

Year:

2010

Language:

english

File:

PDF, 383 KB

english, 2010

34

17-P041 Transcriptome analysis of FGF signalling in embryonic stem cells

Theodora Tzanavari, Alexei A. Sharov, Emma A. Hall, Yulan Piao, Nicola Drummond, Austin Smith, Minoru S.H. Ko, Tilo Kunath

Journal:

Mechanisms of Development

Year:

2009

Language:

english

File:

PDF, 46 KB

english, 2009

35

Bayesian Coalescent Inference of Major Human Mitochondrial DNA Haplogroup Expansions in Africa

Quentin D. Atkinson, Russell D. Gray and Alexei J. Drummond

Journal:

Proceedings Biological Sciences

Year:

2009

Language:

english

File:

PDF, 1.16 MB

english, 2009

36

Evidence for Time Dependency of Molecular Rate Estimates

Ho, Simon Y. W., Shapiro, Beth, Phillips, Matthew J., Cooper, Alan, Drummond, Alexei J.

Journal:

Systematic Biology

Year:

2007

Language:

english

File:

PDF, 1.32 MB

english, 2007

37

[IEEE 2008 8th IEEE International Conference on Bioinformatics and BioEngineering (BIBE) - Athens, Greece (2008.10.8-2008.10.10)] 2008 8th IEEE International Conference on BioInformatics and BioEngineering - Clock-constrained tree proposal operators in Bayesian phylogenetic inference

Hohna, Sebastian, Defoin-Platel, Michael, Drummond, Alexei J.

Year:

2008

Language:

english

File:

PDF, 2.64 MB

english, 2008

38

Simulating gene trees under the multispecies coalescent and time-dependent migration

Joseph Heled,David Bryant,Alexei J Drummond

Journal:

BMC Evolutionary Biology

Year:

2013

Language:

english

File:

PDF, 458 KB

english, 2013

39

The founding charter of the Genomic Observatories Network

Davies, Neil, Field, Dawn, Amaral-Zettler, Linda, Clark, Melody S, Deck, John, Drummond, Alexei, Faith, Daniel P, Geller, Jonathan, Gilbert, Jack, Glöckner, Frank, Hirsch, Penny R, Leong, Jo-Ann, Meye

Journal:

Year:

2014

Language:

english

File:

PDF, 264 KB

english, 2014

40

Relaxed Phylogenetics and Dating with Confidence

Drummond, Alexei J., Ho, Simon Y. W., Phillips, Matthew J., Rambaut, Andrew

Journal:

Year:

2006

Language:

english

File:

PDF, 315 KB

english, 2006

41

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates

Vrancken, Bram, Rambaut, Andrew, Suchard, Marc A., Drummond, Alexei, Baele, Guy, Derdelinckx, Inge, Van Wijngaerden, Eric, Vandamme, Anne-Mieke, Van Laethem, Kristel, Lemey, Philippe, Fraser, Christop

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 798 KB

english, 2014

42

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

Lemey, Philippe, Kosakovsky Pond, Sergei L., Drummond, Alexei J., Pybus, Oliver G., Shapiro, Beth, Barroso, Helena, Taveira, Nuno, Rambaut, Andrew

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 517 KB

english, 2007

43

Bayesian Phylogeography Finds Its Roots

Lemey, Philippe, Rambaut, Andrew, Drummond, Alexei J., Suchard, Marc A., Fraser, Christophe

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 5.85 MB

english, 2009

44

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

Gavryushkina, Alexandra, Welch, David, Stadler, Tanja, Drummond, Alexei J., Koelle, Katia

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 724 KB

english, 2014

45

Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2

Wertheim, Joel O., Worobey, Michael, Drummond, Alexei J.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 354 KB

english, 2009

46

Evaluating a multigene environmental DNA approach for biodiversity assessment

Drummond, Alexei J., Newcomb, Richard D., Buckley, Thomas R., Xie, Dong, Dopheide, Andrew, Potter, Benjamin CM, Heled, Joseph, Ross, Howard A., Tooman, Leah, Grosser, Stefanie, Park, Duckchul, Demetra

Journal:

Year:

2015

Language:

english

File:

PDF, 3.59 MB

english, 2015

47

Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods

Ogilvie, Huw A., Heled, Joseph, Xie, Dong, Drummond, Alexei J.

Journal:

Systematic Biology

Year:

2016

Language:

english

File:

PDF, 2.57 MB

english, 2016

48

Phylodynamics with migration: A computational framework to quantify population structure from genomic data

Kühnert, Denise, Stadler, Tanja, Vaughan, Timothy G., Drummond, Alexei J.

Journal:

Molecular Biology and Evolution

Year:

2016

Language:

english

File:

PDF, 469 KB

english, 2016

49

The space of ultrametric phylogenetic trees

Gavryushkin, Alex, Drummond, Alexei J.

Journal:

Journal of Theoretical Biology

Year:

2016

Language:

english

File:

PDF, 1015 KB

english, 2016

50

Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012.

Davies, Neil, Field, Dawn, Amaral-Zettler, Linda, Barker, Katharine, Bicak, Mesude, Bourlat, Sarah, Coddington, Jonathan, Deck, John, Drummond, Alexei, Gilbert, Jack A., Glöckner, Frank Oliver, Kottma

Journal:

Standards in Genomic Sciences

Year:

2014

Language:

english

File:

PDF, 321 KB

english, 2014