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Preprints

  1. Lars Berling, Jonathan Klawitter, Remco Bouckaert, Dong Xie, Alex Gavryushkin, Alexei J Drummond (2024) Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities. bioRxiv, 2024-02.  doi:10.1101/2024.02.20.581316
  2. Jonathan Klawitter, Remco R Bouckaert, Alexei J Drummond (2024) Skeletons in the Forest: Using Entropy-Based Rogue Detection on Bayesian Phylogenetic Tree Distributions. bioRxiv, 2024-09.  doi:10.1101/2024.09.25.615070
  3. Fabio K Mendes, Remco Bouckaert, Luiz M Carvalho, Alexei J Drummond (2024) How to validate a Bayesian evolutionary model. bioRxiv, 2024-02.  doi:10.1101/2024.02.11.579856
  4. Alexei J Drummond, Kylie Chen, Fábio K Mendes, Dong Xie (2022) LinguaPhylo: a probabilistic model specification language for reproducible phylogenetic analyses. bioRxiv.  doi:10.1101/2022.08.08.503246
  5. Christiaan Swanepoel, Mathieu Fourment, Xiang Ji, Hassan Nasif, Marc A Suchard, Frederick A Matsen IV, Alexei Drummond (2022) TreeFlow: probabilistic programming and automatic differentiation for phylogenetics. arXiv preprint arXiv:2211.05220.  doi:10.48550/arXiv.2211.05220
  6. Alexei Drummond, Alex Popinga (2021) Bayesian inference of the climbing grade scale. arXiv Statistics Applications.  https://arxiv.org/abs/2111.08140
  7. Rong Zhang, Alexei J Drummond, Fábio K Mendes (2021) Scalable total-evidence inference from molecular and continuous characters in a Bayesian framework. bioRxiv.  doi:10.1101/2021.04.21.440863
  8. Jordan Douglas, Richard L Kingston, Alexei J Drummond (2019) Approximate Bayesian computation of transcriptional pausing mechanisms. bioRxiv.  doi:10.1101/748210
  9. Nicola Felix Mueller, Huw Ogilvie, Chi Zhang, Alexei Drummond, Tanja Stadler (2018) Inference of species histories in the presence of gene flow. bioRxiv.  doi:10.1101/348391

Peer-reviewed journal articles

  1. Rong Zhang, Alexei J Drummond, Fábio K Mendes (2024) Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters. Syst Biol 73, 102-124.  doi:10.1093/sysbio/syad067
  2. Alexei J Drummond, Kylie Chen, Fábio K Mendes, Dong Xie (2023) LinguaPhylo: A probabilistic model specification language for reproducible phylogenetic analyses. PLoS Comput Biol 19, e1011226.  doi:10.1371/journal.pcbi.1011226
  3. Cinthy Jimenez-Silva, Ricardo Rivero, Jordan Douglas, Remco Bouckaert, Ch Julian Villabona-Arenas, Katherine E Atkins, Bertha Gastelbondo, Alfonso Calderon, Camilo Guzman, Daniel Echeverri-De la Hoz, Marina Muñoz, Nathalia Ballesteros, Sergio Castañeda, Luz H Patiño, Angie Ramirez, Nicolas Luna, Alberto Paniz-Mondolfi, Hector Serrano-Coll, Juan David Ramirez, Salim Mattar, Alexei J Drummond (2023) Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia. Commun Med (Lond) 3, 97.  doi:10.1038/s43856-023-00328-3
  4. Kylie Chen, Jiří C Moravec, Alex Gavryushkin, David Welch, Alexei J Drummond (2022) Accounting for errors in data improves divergence time estimates in single-cell cancer evolution. Mol Biol Evol.  doi:10.1093/molbev/msac143
  5. Huw A Ogilvie, Fábio K Mendes, Timothy G Vaughan, Nicholas J Matzke, Tanja Stadler, David Welch, Alexei J Drummond (2022) Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales. Syst Biol 71, 208-220.  doi:10.1093/sysbio/syab054
  6. Jordan Douglas, Alexei J Drummond, Richard L Kingston (2021) Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene. Virus Evol 7, veab028.  doi:10.1093/ve/veab028
  7. Jordan Douglas, Fábio K Mendes, Remco Bouckaert, Dong Xie, Cinthy L Jiménez-Silva, Christiaan Swanepoel, Joep de Ligt, Xiaoyun Ren, Matt Storey, James Hadfield, Colin R Simpson, Jemma L Geoghegan, Alexei J Drummond, David Welch (2021) Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations. Virus Evol 7, veab052.  doi:10.1093/ve/veab052
  8. Jemma L Geoghegan, Jordan Douglas, Xiaoyun Ren, Matthew Storey, James Hadfield, Olin K Silander, Nikki E Freed, Lauren Jelley, Sarah Jefferies, Jillian Sherwood, Shevaun Paine, Sue Huang, Andrew Sporle, Michael G Baker, David R Murdoch, Alexei J Drummond, David Welch, Colin R Simpson, Nigel French, Edward C Holmes, Joep de Ligt (2021) Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand. Emerg Infect Dis 27, 1317-1322.  doi:10.3201/eid2705.204579
  9. Tara Swadi, Jemma L Geoghegan, Tom Devine, Caroline McElnay, Jillian Sherwood, Phil Shoemack, Xiaoyun Ren, Matt Storey, Sarah Jefferies, Erasmus Smit, James Hadfield, Aoife Kenny, Lauren Jelley, Andrew Sporle, Andrea McNeill, G Edwin Reynolds, Kip Mouldey, Lindsay Lowe, Gerard Sonder, Alexei J Drummond, Sue Huang, David Welch, Edward C Holmes, Nigel French, Colin R Simpson, Joep de Ligt (2021) Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing. Emerg Infect Dis 27.  doi:10.3201/eid2703.204714
  10. Jordan Douglas, Richard Kingston, Alexei J Drummond (2020) Bayesian inference and comparison of stochastic transcription elongation models. PLoS Comput Biol 16, e1006717.  doi:10.1371/journal.pcbi.1006717
  11. Jemma L Geoghegan, Xiaoyun Ren, Matthew Storey, James Hadfield, Lauren Jelley, Sarah Jefferies, Jill Sherwood, Shevaun Paine, Sue Huang, Jordan Douglas, Fábio K Mendes, Andrew Sporle, Michael G Baker, David R Murdoch, Nigel French, Colin R Simpson, David Welch, Alexei J Drummond, Edward C Holmes, Sebastián Duchêne, Joep de Ligt (2020) Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand. Nat Commun 11, 6351.  doi:10.1038/s41467-020-20235-8
  12. Rong Zhang, Alexei Drummond (2020) Improving the performance of Bayesian phylogenetic inference under relaxed clock models. BMC Evolutionary Biology 20, 1-28.  doi:10.1186/s12862-020-01609-4
  13. Remco Bouckaert, Timothy G Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K Mendes, Nicola F Müller, Huw A Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David Rasmussen, Igor Siveroni, Marc A Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, Alexei J Drummond (2019) BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol 15, e1006650.  doi:10.1371/journal.pcbi.1006650
  14. Andrew Dopheide, Leah K Tooman, Stefanie Grosser, Barbara Agabiti, Birgit Rhode, Dong Xie, Mark I Stevens, Nicola Nelson, Thomas R Buckley, Alexei J Drummond, Richard D Newcomb (2019) Estimating the biodiversity of terrestrial invertebrates on a forested island using DNA barcodes and metabarcoding data. Ecol Appl, e01877.  doi:10.1002/eap.1877
  15. Andrew Dopheide, Dong Xie, Thomas R. Buckley, Alexei J Drummond, Richard D. Newcomb (2019) Impacts of DNA extraction and PCR on DNA metabarcoding estimates of soil biodiversity. Methods in Ecology and Evolution 10, 120-133.  doi:10.1111/2041-210X.13086
  16. Sebastian Duchene, Remco Bouckaert, David A Duchene, Tanja Stadler, Alexei J Drummond (2019) Phylodynamic Model Adequacy Using Posterior Predictive Simulations. Syst Biol 68, 358-364.  doi:10.1093/sysbio/syy048
  17. Abbas Jariani, Christopher Warth, Koen Deforche, Pieter Libin, Alexei J Drummond, Andrew Rambaut, Frederick A Matsen Iv, Kristof Theys (2019) SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination. Virus Evol 5, vez003.  doi:10.1093/ve/vez003
  18. Timothy G Vaughan, Gabriel E Leventhal, David A Rasmussen, Alexei J Drummond, David Welch, Tanja Stadler (2019) Estimating Epidemic Incidence and Prevalence from Genomic Data. Mol Biol Evol 36, 1804-1816.  doi:10.1093/molbev/msz106
  19. Jing Yang, Nicola F Müller, Remco Bouckaert, Bing Xu, Alexei J Drummond (2019) Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration. PLoS Comput Biol 15, e1007189.  doi:10.1371/journal.pcbi.1007189
  20. Jing Yang, Dong Xie, Zhen Nie, Bing Xu, Alexei J Drummond (2019) Inferring host roles in bayesian phylodynamics of global avian influenza A virus H9N2. Virology 538, 86-96.  doi:10.1016/j.virol.2019.09.011
  21. J Barido-Sottani, V Bošková, LD Plessis, D Kühnert, C Magnus, V Mitov, NF Müller, J Pečerska, DA Rasmussen, C Zhang, AJ Drummond, TA Heath, OG Pybus, TG Vaughan, T Stadler (2018) Taming the BEAST - A Community Teaching Material Resource for BEAST 2. Systematic biology 67, 170-174.  doi:10.1093/sysbio/syx060
  22. Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard (2018) Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Systematic biology 67, 901-904.  doi:10.1093/sysbio/syy032
  23. T Stadler, A Gavryushkina, RCM Warnock, AJ Drummond, TA Heath (2018) The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes. Journal of Theoretical Biology 447, 41-55.  doi:10.1016/j.jtbi.2018.03.005
  24. Marc A Suchard, Philippe Lemey, Guy Baele, Daniel L Ayres, Alexei J Drummond, Andrew Rambaut (2018) Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol 4, vey016.  doi:10.1093/ve/vey016
  25. C Zhang, HA Ogilvie, AJ Drummond, T Stadler (2018) Bayesian Inference of Species Networks from Multilocus Sequence Data. Molecular Biology and Evolution 35, 504-517.  doi:10.1093/molbev/msx307
  26. RR Bouckaert, AJ Drummond (2017) bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evolutionary Biology 17.  doi:10.1186/s12862-017-0890-6
  27. A Gavryushkina, TA Heath, DT Ksepka, T Stadler, D Welch, AJ Drummond (2017) Bayesian total-evidence dating reveals the recent crown radiation of penguins. Systematic Biology 66, 57-73.  doi:10.1093/sysbio/syw060
  28. HA Ogilvie, RR Bouckaert, AJ Drummond (2017) StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates. Molecular Biology and Evolution 34, 2101-2114.  doi:10.1093/molbev/msx126
  29. TG Vaughan, D Welch, AJ Drummond, PJ Biggs, T George, NP French (2017) Inferring ancestral recombination graphs from bacterial genomic data. Genetics 205, 857-870.  doi:10.1534/genetics.116.193425
  30. AJ Drummond, T Stadler (2016) Bayesian phylogenetic estimation of fossil ages. Philosophical Transactions of the Royal Society B: Biological Sciences 371.  doi:10.1098/rstb.2015.0129
  31. A Gavryushkin, AJ Drummond (2016) The space of ultrametric phylogenetic trees. Journal of theoretical biology 403, 197-208.  doi:10.1016/j.jtbi.2016.05.001
  32. D Kühnert, T Stadler, TG Vaughan, AJ Drummond (2016) Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data. Molecular biology and evolution 33, 2102-2116.  doi:10.1093/molbev/msw064
  33. HA Ogilvie, J Heled, D Xie, AJ Drummond (2016) Computational performance and statistical accuracy of ∗BEAST and comparisons with other methods. Systematic Biology 65, 381-396.  doi:10.1093/sysbio/syv118
  34. AJ Drummond, RD Newcomb, TR Buckley, D Xie, A Dopheide, BCM Potter, J Heled, HA Ross, L Tooman, S Grosser, D Park, NJ Demetras, MI Stevens, JC Russell, SH Anderson, A Carter, N Nelson (2015) Evaluating a multigene environmental DNA approach for biodiversity assessment. GigaScience 4.  doi:10.1186/s13742-015-0086-1
  35. J Heled, AJ Drummond (2015) Calibrated birth-death phylogenetic time-tree priors for bayesian inference. Systematic biology 64, 369-383.  doi:10.1093/sysbio/syu089
  36. A Popinga, T Vaughan, T Stadler, AJ Drummond (2015) Inferring epidemiological dynamics with Bayesian coalescent inference: The merits of deterministic and stochastic models. Genetics 199, 595-607.  doi:10.1534/genetics.114.172791
  37. T Stadler, TG Vaughan, A Gavryushkin, S Guindon, D Kühnert, GE Leventhal, AJ Drummond (2015) How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?. Proceedings. Biological sciences 282, 20150420.  doi:10.1098/rspb.2015.0420
  38. R Bouckaert, J Heled, D Kühnert, T Vaughan, CH Wu, D Xie, MA Suchard, A Rambaut, AJ Drummond (2014) BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Computational Biology 10.  doi:10.1371/journal.pcbi.1003537
  39. N Davies, D Field, L Amaral-Zettler, K Barker, M Bicak, S Bourlat, J Coddington, J Deck, A Drummond, JA Gilbert, FO Glöckner, R Kottmann, C Meyer, N Morrison, M Obst, R Robbins, L Schriml, P Sterk, S Stones-Havas (2014) Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012. Standards in Genomic Sciences 9, 1236-1250.  doi:10.4056/sigs.4319681
  40. N Davies, D Field, L Amaral-Zettler, MS Clark, J Deck, A Drummond, DP Faith, J Geller, J Gilbert, FO Glöckner, PR Hirsch, J-A Leong, C Meyer, M Obst, S Planes, C Scholin, AP Vogler, RD Gates, R Toonen, V Berteaux-Lecellier, M Barbier, K Barker, S Bertilsson, M Bicak, MJ Bietz, J Bobe, L Bodrossy, A Borja, J Coddington, J Fuhrman, G Gerdts, R Gillespie, K Goodwin, PC Hanson, J-M Hero, D Hoekman, J Jansson, C Jeanthon, R Kao, A Klindworth, R Knight, R Kottmann, MS Koo, G Kotoulas, AJ Lowe, VT Marteinsson, F Meyer, N Morrison, DD Myrold, E Pafilis, S Parker, JJ Parnell, PN Polymenakou, S Ratnasingham, GK Roderick, N Rodriguez-Ezpeleta, K Schonrogge, N Simon, NJ Valette-Silver, YP Springer, GN Stone, S Stones-Havas, S-A Sansone, KM Thibault, P Wecker, A Wichels, JC Wooley, T Yahara, A Zingone, GOs-COS (2014) The founding charter of the Genomic Observatories Network. GigaScience 3, 2.  doi:10.1186/2047-217x-3-2
  41. A Gavryushkina, D Welch, T Stadler, AJ Drummond (2014) Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Computational Biology 10.  doi:10.1371/journal.pcbi.1003919
  42. D Kühnert, T Stadler, TG Vaughan, AJ Drummond (2014) Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model. Journal of the Royal Society Interface 11.  doi:10.1098/rsif.2013.1106
  43. TG Vaughan, D Kühnert, A Popinga, D Welch, AJ Drummond (2014) Efficient Bayesian inference under the structured coalescent. Bioinformatics 30, 2272-2279.  doi:10.1093/bioinformatics/btu201
  44. B Vrancken, A Rambaut, MA Suchard, A Drummond, G Baele, I Derdelinckx, E Van Wijngaerden, A-M Vandamme, K Van Laethem, P Lemey (2014) The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates. PLoS computational biology 10, e1003505.  doi:10.1371/journal.pcbi.1003505
  45. G Baele, WLS Li, A Drummond, MA Suchard, P Lemey (2013) Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics. Molecular Biology and Evolution 30, 239-243.  doi:10.1093/molbev/mss243
  46. J Bahl, S Krauss, D Kühnert, M Fourment, G Raven, SP Pryor, LJ Niles, A Danner, D Walker, IH Mendenhall, YCF Su, VG Dugan, RA Halpin, TB Stockwell, RJ Webby, DE Wentworth, AJ Drummond, GJD Smith, Webster RG (2013) Influenza a virus migration and persistence in North American wild birds. PLoS pathogens 9, e1003570.  doi:10.1371/journal.ppat.1003570
  47. A Gavryushkina, D Welch, AJ Drummond (2013) Recursive algorithms for phylogenetic tree counting. Algorithms for Molecular Biology 8.  doi:10.1186/1748-7188-8-26
  48. J Heled, D Bryant, AJ Drummond (2013) Simulating gene trees under the multispecies coalescent and time-dependent migration. BMC evolutionary biology 13, 44.  doi:10.1186/1471-2148-13-44
  49. T Stadler, D Kuehnert, S Bonhoeffer, AJ Drummond (2013) Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proceedings of the National Academy of Sciences of the United States of America 110, 228-233.  doi:10.1073/pnas.1207965110
  50. TG Vaughan, AJ Drummond (2013) A stochastic simulator of birth-death master equations with application to phylodynamics. Molecular biology and evolution 30, 1480-1493.  doi:10.1093/molbev/mst057
  51. C-H Wu, MA Suchard, A Drummond (2013) Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments. Molecular Biology and Evolution 30, 669-688.  doi:10.1093/molbev/mss258
  52. R Bouckaert, P Lemey, M Dunn, SJ Greenhill, AV Alekseyenko, AJ Drummond, RD Gray, MA Suchard, QD Atkinson (2012) Mapping the origins and expansion of the Indo-European language family. Science 337, 957-960.  doi:10.1126/science.1219669
  53. AJ Drummond, MA Suchard, D Xie, A Rambaut (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29, 1969-1973.  doi:10.1093/molbev/mss075
  54. J Heled, AJ Drummond (2012) Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation. Systematic Biology 61, 138-149.  doi:10.1093/sysbio/syr087
  55. S Höhna, AJ Drummond (2012) Guided tree topology proposals for Bayesian phylogenetic inference. Systematic biology 61, 1-11.  doi:10.1093/sysbio/syr074
  56. M Kearse, R Moir, A Wilson, S Stones-Havas, M Cheung, S Sturrock, S Buxton, A Cooper, S Markowitz, C Duran, T Thierer, B Ashton, P Meintjes, A Drummond (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647-1649.  doi:10.1093/bioinformatics/bts199
  57. WLS Li, AJ Drummond (2012) Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics. Molecular Biology and Evolution 29, 751-761.  doi:10.1093/molbev/msr232
  58. T Stadler, R Kouyos, V von Wyl, S Yerly, J Böni, P Bürgisser, T Klimkait, B Joos, P Rieder, D Xie, HF Günthard, AJ Drummond, S Bonhoeffer, Swiss HIV Cohort Study (2012) Estimating the Basic Reproductive Number from Viral Sequence Data. Molecular Biology and Evolution 29, 347-357.  doi:10.1093/molbev/msr217
  59. TG Vaughan, PD Drummond, A Drummond (2012) Within-host demographic fluctuations and correlations in early retroviral infection. Journal of Theoretical Biology 295, 86-99.  doi:10.1016/j.jtbi.2011.11.016
  60. D Kühnert, C-H Wu, AJ Drummond (2011) Phylogenetic and epidemic modeling of rapidly evolving infectious diseases. Infection, genetics and evolution 11, 1825-1841.  doi:10.1016/j.meegid.2011.08.005
  61. B Shapiro, SYW Ho, AJ Drummond, MA Suchard, OG Pybus, A Rambaut (2011) A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages. Molecular Biology and Evolution 28, 879-887.  doi:10.1093/molbev/msq262
  62. C-H Wu, AJ Drummond (2011) Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo. Genetics 188, 151-164.  doi:10.1534/genetics.110.125260
  63. SN Bennett, AJ Drummond, DD Kapan, MA Suchard, JL Muñoz-Jordán, OG Pybus, EC Holmes, DJ Gubler (2010) Epidemic Dynamics Revealed in Dengue Evolution. Molecular biology and evolution 27, 811-818.  doi:10.1093/molbev/msp285
  64. AJ Drummond, MA Suchard (2010) Bayesian random local clocks, or one rate to rule them all. BMC biology 8, 114.  doi:10.1186/1741-7007-8-114
  65. PD Drummond, TG Vaughan, AJ Drummond (2010) Extinction times in autocatalytic systems. The journal of physical chemistry. A 114, 10481-10491.  doi:10.1021/jp104471e
  66. SJ Greenhill, AJ Drummond, RD Gray (2010) How accurate and robust are the phylogenetic estimates of Austronesian language relationships?. PloS one 5, e9573.  doi:10.1371/journal.pone.0009573
  67. J Heled, AJ Drummond (2010) Bayesian Inference of Species Trees from Multilocus Data. Molecular Biology and Evolution 27, 570-580.  doi:10.1093/molbev/msp274
  68. TG Vaughan, PD Drummond, AJ Drummond (2010) A retrodictive stochastic simulation algorithm. Journal of Computational Physics 229, 3777-3791.  doi:10.1016/j.jcp.2010.01.027 [pdf]
  69. QD Atkinson, RD Gray, AJ Drummond (2009) Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa. Proceedings of the Royal Society of London Series B - Biological Sciences 276, 367-373.  doi:10.1098/rspb.2008.0785
  70. M Bunce, TH Worthy, MJ Phillips, RN Holdaway, E Willerslev, J Haile, B Shapiro, RP Scofield, A Drummond, PJJ Kamp (2009) The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Proceedings of the National Academy of Sciences of the United States of America 106, 20646-20651.  doi:10.1073/pnas.0906660106
  71. RD Gray, AJ Drummond, SJ Greenhill (2009) Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science 323, 479-483.  doi:10.1126/science.1166858
  72. P Lemey, A Rambaut, AJ Drummond, MT Suchard (2009) Bayesian Phylogeography Finds its Roots. PLoS Computational Biology 5.  doi:10.1371/journal.pcbi.1000520
  73. A Rambaut, SY Ho, AJ Drummond, B Shapiro (2009) Accomodating the Effect of Ancient DNA Damage on Inferences of Demographic Histories. Molecular Biology and Evolution 26.  doi:10.1093/molbev/msn256
  74. QD Atkinson, RD Gray, AJ Drummond (2008) mtDNA Variation Predicts Population Size in Humans and Reveals a Major Southern Asian Chapter in Human Prehistory. Molecular Biology and Evolution 25, 468-474.  doi:10.1093/molbev/msm277
  75. AJ Drummond, MT Suchard (2008) Fully Bayesian tests of neutrality using genealogical summary statistics. BMC Genetics 9.  doi:10.1186/1471-2156-9-68
  76. J Heled, AJ Drummond (2008) Bayesian inference of population size history from multiple loci. BMC Evolutionary Biology 8.  doi:10.1186/1471-2148-8-289
  77. CC Hon, TY Lam, ZL Shi, AJ Drummond, CW Yip, F Zeng, PY Lam, FC Leung (2008) Evidence of the Recombinant Origin of A Bat SARS-like Coronavirus and its Implications on the Direct Ancestor of SARS Coronavirus. Journal of Virology 82, 1819-1826.  doi:10.1128/JVI.01926-07
  78. AJ Drummond, A Rambaut (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7, 1-8.  doi:10.1186/1471-2148-7-214
  79. SY Ho, B Shapiro, MJ Phillips, A Cooper, AJ Drummond (2007) Evidence for Time Dependency of Molecular Rate Estimates. Systematic Biology 56, 515-522.  doi:10.1080/10635150701435401
  80. P Lemey, SL Kosakovsky Pond, AJ Drummond, OG Pybus, B Shapiro, H Barroso, N Taveira, A Rambaut (2007) Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics. PLoS Computational Biology 3, 282-292.  doi:10.1371/journal.pcbi.0030029
  81. OG Pybus, A Rambaut, R Belshaw, RP Freckleton, AJ Drummond, EC Holmes (2007) Phylogenetic Evidence for Deleterious Mutation Load in RNA Viruses and Its Contribution to Viral Evolution. Molecular Biology and Evolution 24, 845-852.  doi:10.1093/molbev/msm001
  82. R Biek, AJ Drummond, M Poss (2006) A virus reveals population structure and recent demographic history of its carnivore host. Science 311, 538-541.  doi:10.1126/science.1121360
  83. AJ Drummond, SY Ho, MJ Phillips, A Rambaut (2006) Relaxed phylogenetics and dating with confidence. PLOS Biology 4, 699-710.  doi:10.1371/journal.pbio.0040088
  84. CT Edwards, EC Holmes, OG Pybus, DJ Wilson, RP Viscidi, EJ Abrams, RE Phillips, AJ Drummond (2006) Evolution of the Human Immunodeficiency Virus Envelope Gene Is Dominated by Purifying Selection. Genetics 174, 1441-1453.  doi:10.1534/genetics.105.052019
  85. CT Edwards, EC Holmes, DJ Wilson, RP Viscidi, EJ Abrams, RE Phillips, AJ Drummond (2006) Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1. BMC Evolutionary Biology 6.  doi:10.1186/1471-2148-6-28
  86. CC Hon, TY Lam, AJ Drummond, A Rambaut, YF Lee, CW Yip, F Zeng, PY Lam, PT Ng, FC Leung (2006) Phylogenetic Analysis Reveals a Correlation between the Expansion of Very Virulent Infectious Bursal Disease Virus and Reassortment of Its Genome Segment B. Journal of Virology 80.  doi:10.1128/JVI.00585-06
  87. B Shapiro, A Rambaut, AJ Drummond (2006) Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences. Molecular Biology and Evolution 23, 7-9.  doi:10.1093/molbev/msj021
  88. J Strugnell, JA Jackson, AJ Drummond, A Cooper (2006) Divergence time estimates for major cephalopod groups: evidence from multiple genes. Cladistics-The International Journal of the Willi Hennig Society 22, 89-96.  doi:10.1111/j.1096-0031.2006.00086.x
  89. AJ Drummond, A Rambaut, B Shapiro, OG Pybus (2005) Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences. Molecular Biology and Evolution 22, 1185-1192.  doi:10.1093/molbev/msi103
  90. R Forsberg, AJ Drummond, J Hein (2005) Tree measures and the number of segregating sites in time-structured population samples. BMC Genetics 6.  doi:10.1186/1471-2156-6-35
  91. MT Gilbert, B Shapiro, A Drummond, A Cooper (2005) Post-mortem DNA damage hotspots in Bison (Bison bison) provide evidence for both damage and mutational hotspots in human mitochondrial DNA. Journal of Archaeological Science 32, 1053-1060.  doi:10.1016/j.jas.2005.02.006
  92. SY Ho, MJ Phillips, A Cooper, AJ Drummond (2005) Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times. Molecular Biology and Evolution 22, 1561-1568.  doi:10.1093/molbev/msi145
  93. SY Ho, MJ Phillips, AJ Drummond, A Cooper (2005) Accuracy of Rate Estimation Using Relaxed-Clock Models with a Critical Focus on the Early Metazoan Radiation. Molecular Biology and Evolution 22, 1355-1363.  doi:10.1093/molbev/msi125
  94. G Lunter, I Miklos, AJ Drummond, JL Jensen, J Hein (2005) Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics 6, 8.  doi:10.1186/1471-2105-6-83
  95. J Strugnell, M Norman, J Jackson, AJ Drummond, A Cooper (2005) Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework. Molecular phylogenetics and evolution 37, 426-441.  doi:10.1016/j.ympev.2005.03.020
  96. A Cooper, AJ Drummond, E Willerslev (2004) Ancient DNA: Would the Real Neanderthal Please Stand Up?. Current Biology 14, R431-R433.  doi:10.1016/j.cub.2004.05.037
  97. AJ Drummond (2004) Inferring Phylogenies: an instant classic. Heredity 93, 519-519.  doi:10.1038/sj.hdy.6800575
  98. P Lemey, OG Pybus, A Rambaut, AJ Drummond, DL Robertson, P Roques, A Vandamme (2004) The Molecular Population Genetics of HIV-1 Group O. Genetics 167, 1059-1068.  doi:10.1534/genetics.104.026666
  99. B Shapiro, AJ Drummond, A Rambaut, MC Wilson, PE Matheus, AV Sher, OG Pybus, MT Gilbert, I Barnes, E Binladen J Willerslev, AJ Hansen, GF Baryshnikov, JA Burns, S Davydov, JC Driver, DG Froese, R C. Harington, G Keddie, P Kosintsev, ML Kunz, LD Martin, RO Stephenson, J Storer, R Tedford, S Zimov, A Cooper (2004) Rise and Fall of the Beringian Steppe Bison. Science 306, 1561-1565.  doi:10.1126/science.1101074
  100. J Strugnell, M Norman, AJ Drummond, A Cooper (2004) Neotenous origins of pelagic octopuses. Current Biology 14, R300-R301.  doi:10.1016/j.cub.2004.03.048
  101. R Biek, AG Rodrigo, D Holley, A Drummond, CRJ Anderson, HA Ross, M Poss (2003) Epidemiology, Genetic Diversity, and Evolution of Endemic Feline Immunodeficiency Virus in a Population of Wild Cougars. Journal of Virology 77, 9578-9589.  doi:10.1128/JVI.77.17.9578-9589.2003
  102. M Bunce, TH Worthy, T Ford, W Hoppit, E Willerslev, AJ Drummond, A Cooper (2003) Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 425, 172-175.  doi:10.1038/nature01871
  103. Alexei Drummond, Geoff Nicholls (2003) Discussion on the Paper by Wilson, Weale and Balding. Journal of the Royal Statistical Society: Series A (Statistics in Society) 166, 188-201.  doi:10.1111/1467-985X.00265
  104. Alexei Drummond, Oliver G Pybus, Andrew Rambaut (2003) Inference of Viral Evolutionary Rates from Molecular Sequences. Advances in Parasitology 54, 331-358.  doi:10.1016/S0065-308X(03)54008-8 [pdf]
  105. AJ Drummond, OG Pybus, A Rambaut, R Forsberg, AG Rodrigo (2003) Measurably evolving populations. Trends in Ecology and Evolution 18, 481-488.  doi:10.1016/S0169-5347(03)00216-7
  106. G Lunter, I Miklos, AJ Drummond, JL Jensen, J Hein (2003) Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model. Algorithms in Bioinformatics 2812, 228-244.  doi:10.1007/978-3-540-39763-2_18
  107. OG Pybus, AJ Drummond, T Nakano, BH Robertson, A Rambaut (2003) The Epidemiology and Iatrogenic Transmission of Hepatitis C Virus in Egypt: A Bayesian Coalescent Approach. Molecular Biology and Evolution 20, 381-387.  doi:10.1093/molbev/msg043
  108. AG Rodrigo, MG Goode, R Forsberg, HA Ross, AJ Drummond (2003) Inferring Evolutionary Rates Using Serially Sampled Sequences from Several Populations. Molecular Biology and Evolution 20, 2010-2018.  doi:10.1093/molbev/msg215
  109. AJ Drummond, GK Nicholls, AG Rodrigo, W Solomon (2002) Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data. Genetics 161, 1307-1320.  http://www.genetics.org/content/161/3/1307
  110. DM Lambert, PA Ritchie, CD Millar, B Holland, A Drummond, C Baroni (2002) Rates of Evolution in Ancient DNA from Adélie Penguins. Science 295, 2270-2273.  doi:10.1126/science.1068105
  111. A Drummond, R Forsberg, AG Rodrigo (2001) The inference of stepwise changes in substitution rates using serial sequence samples. Molecular Biology and Evolution 18, 1365-1371.  doi:10.1093/oxfordjournals.molbev.a003920
  112. AJ Drummond, K Strimmer (2001) PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 17, 662-663.  doi:10.1093/bioinformatics/17.7.662
  113. A Drummond, AG Rodrigo (2000) Reconstructing Genealogies of Serial Samples Under the Assumption of a Molecular Clock Using Serial-Sample UPGMA. Molecular Biology and Evolution 17, 1807-1815.  doi:10.1093/oxfordjournals.molbev.a026281

Conference proceedings and book chapters

  1. S Hoehna, M Defoin-Platel, AJ Drummond (2008) Clock-constrained tree proposal operators in Bayesian phylogenetic inference. In Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering, 1-7.  doi:10.1109/BIBE.2008.4696663 [pdf]
  2. S Hoehna, AJ Drummond (2008) Evaluation of Proposal Distributions on Clock-Constrained Trees in Bayesian Phylogenetic Inference. In Proceedings of the New Zealand Computer Science Research Student Conference (NZCSRSC 2008), 41-48.  [pdf]
  3. S Markowitz, A Drummond, K Nieselt, PR Wills (2006) Simulation model of prebiotic evolution of genetic coding. In Proceedings of Artificial Life X, 152-157.  [pdf]
  4. Gerton Lunter, Alexei J Drummond, István Miklós, Jotun Hein (2005) Statistical alignment: Recent progress, new applications, and challenges. In Statistical methods in molecular evolution, 375-405.  doi:10.1007/0-387-27733-1_14 [pdf]
  5. Alexei Drummond, Geoff K Nicholls, Allen G Rodrigo, Wiremu Solomon (2004) Genealogies from time-stamped sequence data. In Tools for Constructing Chronologies, 149-171.  doi:10.1007/978-1-4471-0231-1_7 [pdf]
  6. Matthew Goode, Korbinian Strimmer, Alexei Drummond, Ed Buckler, Allen Rodrigo (2004) A Brief Introduction to the Phylogenetic Analysis Library Version 1.5. In Proceedings of the Second Conference on Asia-Pacific Bioinformatics 29, 175-179.  http://dl.acm.org/citation.cfm?id=976520.976544 [pdf]

Books

  1. Alexei J Drummond, Remco R Bouckaert (2015) Bayesian evolutionary analysis with BEAST. Cambridge University Press.  doi:10.1017/CBO9781139095112 [pdf]

Doctoral Thesis

  • Alexei J Drummond (2002) Computational Statistical Inference for Molecular Evolution and Population Genetics. PhD thesis. University of Auckland.  http://hdl.handle.net/2292/1053