Dr Alexei Drummond

Communing with nature

@alexeidrummond    Google Citations

Alexei completed his BSc (1996) and PhD in Bioinformatics (2002) at the University of Auckland. He then spent 3 years at the University of Oxford doing post-doctoral research in the Department of Statistics and the Department of Zoology before returning to the University of Auckland in 2005 to take up a Lecturership in Bioinformatics in the Department of Computer Science. Alexei’s research interests are centered around probabilistic models of molecular evolution and population genetics.

Employment history

  • Feb 2013- present, Professor, Department of Computer Science, University of Auckland
  • Feb 2009 – Jan 2013, Associate Professor, Department of Computer Science, University of Auckland
  • Feb 2007 – Jan 2009, Senior Lecturer, Department of Computer Science, University of Auckland
  • Nov 2006 – present, Director, Biomatters Ltd
  • July 2005 – Sep 2008, Chief Scientist, Biomatters Ltd
  • Jul 2005 – Jan 2007, Lecturer, Department of Computer Science, University of Auckland
  • Dec 2003 – Jun 2005, Postdoc, Evolutionary Biology Group, Department of Zoology, University of Oxford
  • Jun 2002- Dec 2003, Postdoc, The Genome Analysis & Bioinformatics Group, Department of Statistics, University of Oxford
  • Jun 2002- Dec 2003, Postdoc, Ancient Biomolecules Centre, Department of Zoology, University of Oxford
  • Dec 1996 – Feb 1998, Software developer, Peace Software, Auckland, NZ

Education

  • 2002, PhD in Bioinformatics, School of Biological Sciences, University of Auckland, Auckland
  • 1996, BSc in Biology and Computer Science, University of Auckland, Auckland

Distinctions/Honours

  • Research Medal, New Zealand Association of Scientists, 2011
  • North and South New Zealander of the Year in Science, 2011
  • Mitchell Prize, International Society for Bayesian Analysis, 2011 [With co-authors]
  • Rutherford Discovery Fellowship, Royal Society of New Zealand, 2010
  • Hamilton Memorial Prize, Royal Society of New Zealand, 2007
  • Best Doctoral Thesis, Faculty of Science, University of Auckland, 2002
  • Society for Systematic Biology, Ernst Mayr Award, 2001
  • New Zealand ACM Programming Competition Overall Champion, 1996

Publications     [ ResearcherID A-3209-2010 | ORCID 0000-0003-4454-2576 ]

2014

Davies, Neil, Dawn Field, Linda Amaral-Zettler, Melody S Clark, John Deck, Alexei Drummond, Daniel P Faith, et al. 2014. “The Founding Charter of the Genomic Observatories Network.” GigaScience 3 (March): 2. doi:10.1186/2047-217X-3-2. (Download)
Popinga, Alex, Tim Vaughan, Tanja Stadler, and Alexei Drummond. 2014. “Bayesian Coalescent Epidemic Inference: Comparison of Stochastic and Deterministic SIR Population Dynamics.” arXiv:1407.1792 [q-Bio], July. http://arxiv.org/abs/1407.1792.
Gavryushkina, Alexandra, David Welch, Tanja Stadler, and Alexei Drummond. 2014. “Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration.” arXiv:1406.4573 [q-Bio], June. http://arxiv.org/abs/1406.4573.
Kühnert, Denise, Tanja Stadler, Timothy G. Vaughan, and Alexei J. 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 (94): 20131106. doi:10.1098/rsif.2013.1106. (Download)
Vrancken, Bram, Andrew Rambaut, Marc A. Suchard, Alexei Drummond, Guy Baele, Inge Derdelinckx, Eric Van Wijngaerden, Anne-Mieke Vandamme, Kristel Van Laethem, and Philippe Lemey. 2014. “The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates.” PLoS Comput Biol 10 (4): e1003505. doi:10.1371/journal.pcbi.1003505.
Vaughan, Timothy G., Denise Kühnert, Alex Popinga, David Welch, and Alexei J. Drummond. 2014. “Efficient Bayesian Inference under the Structured Coalescent.” Bioinformatics, April, btu201. doi:10.1093/bioinformatics/btu201. (Download)
Bouckaert, Remco, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, and Alexei J. Drummond. 2014. “BEAST 2: A Software Platform for Bayesian Evolutionary Analysis.” PLoS Comput Biol 10 (4): e1003537. doi:10.1371/journal.pcbi.1003537.
Davies, Neil, Dawn Field, Linda Amaral-Zettler, Mesude Bicak, Sarah Bourlat, Jonathan Coddington, John Deck, et al. 2014. “Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012.” Standards in Genomic Sciences 9 (3). doi:10.4056/431.

2013

Bahl, Justin, Scott Krauss, Denise Kühnert, Mathieu Fourment, Garnet Raven, S. Paul Pryor, Lawrence J. Niles, et al. 2013. “Influenza A Virus Migration and Persistence in North American Wild Birds.” Edited by Raul Andino. PLoS Pathogens 9 (8): e1003570. doi:10.1371/journal.ppat.1003570.
Heled, Joseph, and Alexei J. Drummond. 2013. “Calibrated Birth-Death Phylogenetic Time-Tree Priors for Bayesian Inference.” arXiv:1311.4921 [q-Bio], November. http://arxiv.org/abs/1311.4921.
Gavryushkina, Alexandra, David Welch, and Alexei J. Drummond. 2013. “Recursive Algorithms for Phylogenetic Tree Counting.” Algorithms for Molecular Biology 8 (1): 26. doi:10.1186/1748-7188-8-26.
Kühnert, Denise, Tanja Stadler, Timothy G. Vaughan, and Alexei J. Drummond. 2013. “Simultaneous Reconstruction of Evolutionary History and Epidemiological Dynamics from Viral Sequences with the Birth-Death SIR Model.” arXiv:1308.5140 [math, Q-Bio, Stat], August. http://arxiv.org/abs/1308.5140.
Vaughan, Timothy G, and Alexei J Drummond. 2013. “A Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics.” Molecular Biology and Evolution 30 (6): 1480–93. doi:10.1093/molbev/mst057. (Download)
Wu, Chieh-Hsi, Marc A Suchard, and Alexei J Drummond. 2013. “Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments.” Molecular Biology and Evolution 30 (3): 669–88. doi:10.1093/molbev/mss258. (Download)
Baele, Guy, Wai Lok Sibon Li, Alexei J. Drummond, Marc A. Suchard, and Philippe Lemey. 2013. “Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics.” Molecular Biology and Evolution 30 (2): 239–43. doi:10.1093/molbev/mss243. (Download)
Stadler, Tanja, Denise Kühnert, Sebastian Bonhoeffer, and Alexei J 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 (1): 228–33. doi:10.1073/pnas.1207965110. (Download)
Heled, Joseph, David Bryant, and Alexei J 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. (Download)

2012

Bouckaert, Remco, Philippe Lemey, Michael Dunn, Simon J Greenhill, Alexander V Alekseyenko, Alexei J Drummond, Russell D Gray, Marc A Suchard, and Quentin D Atkinson. 2012. “Mapping the Origins and Expansion of the Indo-European Language Family.” Science (New York, N.Y.) 337 (6097): 957–60. doi:10.1126/science.1219669.
Drummond, Alexei J, Marc A Suchard, Dong Xie, and Andrew Rambaut. 2012. “Bayesian Phylogenetics with BEAUti and the BEAST 1.7.” Molecular Biology and Evolution 29 (8): 1969–73. doi:10.1093/molbev/mss075.
Kearse, Matthew, Richard Moir, Amy Wilson, Steven Stones-Havas, Matthew Cheung, Shane Sturrock, Simon Buxton, et al. 2012. “Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data.” Bioinformatics (Oxford, England) 28 (12): 1647–49. doi:10.1093/bioinformatics/bts199.
Vaughan, T G, P D Drummond, and A J Drummond. 2012. “Within-Host Demographic Fluctuations and Correlations in Early Retroviral Infection.” Journal of Theoretical Biology 295 (February): 86–99. doi:10.1016/j.jtbi.2011.11.016.
Li, Wai Lok Sibon, and Alexei J Drummond. 2012. “Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics.” Molecular Biology and Evolution 29 (2): 751–61. doi:10.1093/molbev/msr232.
Stadler, Tanja, Roger Kouyos, Viktor von Wyl, Sabine Yerly, Jürg Böni, Philippe Bürgisser, Thomas Klimkait, et al. 2012. “Estimating the Basic Reproductive Number from Viral Sequence Data.” Molecular Biology and Evolution 29 (1): 347–57. doi:10.1093/molbev/msr217.
Höhna, Sebastian, and Alexei J Drummond. 2012. “Guided Tree Topology Proposals for Bayesian Phylogenetic Inference.” Systematic Biology 61 (1): 1–11. doi:10.1093/sysbio/syr074.
Heled, Joseph, and Alexei J Drummond. 2012. “Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation.” Systematic Biology 61 (1): 138–49. doi:10.1093/sysbio/syr087.

2011

Kühnert, Denise, Chieh-Hsi Wu, and Alexei J Drummond. 2011. “Phylogenetic and Epidemic Modeling of Rapidly Evolving Infectious Diseases.” Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases 11 (8): 1825–41. doi:10.1016/j.meegid.2011.08.005.
Wu, Chieh-Hsi, and Alexei J Drummond. 2011. “Joint Inference of Microsatellite Mutation Models, Population History and Genealogies Using Transdimensional Markov Chain Monte Carlo.” Genetics 188 (1): 151–64. doi:10.1534/genetics.110.125260.
Shapiro, Beth, Simon Y W Ho, Alexei J Drummond, Marc A Suchard, Oliver G Pybus, and Andrew Rambaut. 2011. “A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages.” Molecular Biology and Evolution 28 (2): 879–87. doi:10.1093/molbev/msq262.

2010

Drummond, Peter D, Timothy G Vaughan, and Alexei J Drummond. 2010. “Extinction Times in Autocatalytic Systems.” The Journal of Physical Chemistry. A 114 (39): 10481–91. doi:10.1021/jp104471e.
Heled, Joseph, and Alexei J Drummond. 2010. “Bayesian Inference of Species Trees from Multilocus Data.” Molecular Biology and Evolution 27 (3): 570–80. doi:10.1093/molbev/msp274.
Vaughan, TG, PD Drummond, and AJ Drummond. 2010. “A Retrodictive Stochastic Simulation Algorithm.” Journal of Computational Physics 229 (10): 3777–91.
Greenhill, Simon J, Alexei J Drummond, and Russell D Gray. 2010. “How Accurate and Robust Are the Phylogenetic Estimates of Austronesian Language Relationships?” PloS One 5 (3): e9573. doi:10.1371/journal.pone.0009573.
Drummond, Alexei J, and Marc A Suchard. 2010. “Bayesian Random Local Clocks, or One Rate to Rule Them All.” BMC Biology 8: 114. doi:10.1186/1741-7007-8-114.

2009

Bennett, S.N., A.J. Drummond, D.D. Kapan, M.A. Suchard, J.L. Munoz-Jordan, O.G. Pybus, E.C. Holmes, and D.J. Gubler. 2009. “Epidemic Dynamics Revealed in Dengue Evolution.” Molecular Biology and Evolution 27 (4): 811–18. doi:10.1093/molbev/msp285.
Bunce, M., T. H. Worthy, M. J. Phillips, R. N. Holdaway, E. Willerslev, J. Haile, B. Shapiro, et al. 2009. “The Evolutionary History of the Extinct Ratite Moa and New Zealand Neogene Paleogeography.” Proceedings of the National Academy of Sciences 106 (49): 20646–51. doi:10.1073/pnas.0906660106.
Lemey, Philippe, Andrew Rambaut, Alexei J Drummond, and Marc A Suchard. 2009. “Bayesian Phylogeography Finds Its Roots.” PLoS Computational Biology 5 (9): e1000520. doi:10.1371/journal.pcbi.1000520.
Rambaut, Andrew, Simon Y W Ho, Alexei J Drummond, and Beth Shapiro. 2009. “Accommodating the Effect of Ancient DNA Damage on Inferences of Demographic Histories.” Molecular Biology and Evolution 26 (2): 245–48. doi:10.1093/molbev/msn256.
Gray, R. D., A. J. Drummond, and S. J. Greenhill. 2009. “Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement.” Science 323 (5913): 479–83. doi:10.1126/science.1166858.
Atkinson, Quentin D, Russell D Gray, and Alexei J Drummond. 2009. “Bayesian Coalescent Inference of Major Human Mitochondrial DNA Haplogroup Expansions in Africa.” Proceedings. Biological Sciences / The Royal Society 276 (1655): 367–73. doi:10.1098/rspb.2008.0785.

2008

Höhna, Sebastian, Michael Defoin-Platel, and Alexei J. Drummond. 2008. “Clock-Constrained Tree Proposal Operators in Bayesian Phylogenetic Inference.” In , 1–7. IEEE. doi:10.1109/BIBE.2008.4696663.
Hon, Chung-Chau, Tsan-Yuk Lam, Zheng-Li Shi, Alexei J Drummond, Chi-Wai Yip, Fanya Zeng, Pui-Yi Lam, and Frederick Chi-Ching Leung. 2008. “Evidence of the Recombinant Origin of a Bat Severe Acute Respiratory Syndrome (SARS)-like Coronavirus and Its Implications on the Direct Ancestor of SARS Coronavirus.” Journal of Virology 82 (4): 1819–26. doi:10.1128/JVI.01926-07.
Atkinson, Quentin D, Russell D Gray, and Alexei J Drummond. 2008. “mtDNA Variation Predicts Population Size in Humans and Reveals a Major Southern Asian Chapter in Human Prehistory.” Molecular Biology and Evolution 25 (2): 468–74. doi:10.1093/molbev/msm277.
Vaughan, T.G., P.D. Drummond, and A.J. Drummond. 2008. “A New Method for Tackling the Stochastic Dynamics of Viral Infection.”
Höhna, S., and A.J. Drummond. 2008. “Evaluation of Proposal Distributions on Clock-Constrained Trees in Bayesian Phylogenetic Inference.” http://nzcsrsc08.canterbury.ac.nz/site/proceedings/Individual_Papers/pg041_Evaluation_of_Proposal_Distributions_on_Clock-Constrained_Trees.pdf.
Heled, Joseph, and Alexei J Drummond. 2008. “Bayesian Inference of Population Size History from Multiple Loci.” BMC Evolutionary Biology 8: 289. doi:10.1186/1471-2148-8-289.
Drummond, Alexei J, and Marc A Suchard. 2008. “Fully Bayesian Tests of Neutrality Using Genealogical Summary Statistics.” BMC Genetics 9: 68. doi:10.1186/1471-2156-9-68.
Drummond, A.J., and P.D. Drummond. 2008. “Extinction in a Self-Regulating Population with Demographic and Environmental Noise.” Arxiv Preprint ArXiv:0807.4772. http://arxiv.org/abs/0807.4772.

2007

Ho, Simon Y W, Beth Shapiro, Matthew J Phillips, Alan Cooper, and Alexei J Drummond. 2007. “Evidence for Time Dependency of Molecular Rate Estimates.” Systematic Biology 56 (3): 515–22. doi:10.1080/10635150701435401.
Pybus, Oliver G, Andrew Rambaut, Robert Belshaw, Robert P Freckleton, Alexei J Drummond, and Edward C Holmes. 2007. “Phylogenetic Evidence for Deleterious Mutation Load in RNA Viruses and Its Contribution to Viral Evolution.” Molecular Biology and Evolution 24 (3): 845–52. doi:10.1093/molbev/msm001.
Lemey, Philippe, Sergei L Kosakovsky Pond, Alexei J Drummond, Oliver G Pybus, Beth Shapiro, Helena Barroso, Nuno Taveira, and Andrew Rambaut. 2007. “Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics.” PLoS Computational Biology 3 (2): e29. doi:10.1371/journal.pcbi.0030029.
Rodrigo, AG, G. Ewing, and AJ Drummond. 2007. “The Evolutionary Analysis of Measurably Evolving Populations Using Serially Sampled Gene Sequences.” Reconstructing Evolution: New Mathematical and Computational Advances. http://hdl.handle.net/2292/15757.
Rambaut, A., and AJ Drummond. 2007. Tracer. http://beast.bio.ed.ac.uk/Tracer.
Holmes, E. C., and A. J. Drummond. 2007. “The Evolutionary Genetics of Viral Emergence.” In Wildlife and Emerging Zoonotic Diseases: The Biology, Circumstances and Consequences of Cross-Species Transmission, edited by James E. Childs, John S. Mackenzie, and Jürgen A. Richt, 315:51–66. Berlin, Heidelberg: Springer Berlin Heidelberg. http://www.springerlink.com/index/10.1007/978-3-540-70962-6_3.
Drummond, Alexei J, and Andrew Rambaut. 2007. “BEAST: Bayesian Evolutionary Analysis by Sampling Trees.” BMC Evolutionary Biology 7: 214. doi:10.1186/1471-2148-7-214.
Drummond, A.J., and S.Y.W. Ho. 2007. “A Rough Guide to BEAST 1. 4.” Small, 1–41.

2006

Edwards, C. T. T., E. C. Holmes, O. G. Pybus, D. J. Wilson, R. P. Viscidi, E. J. Abrams, R. E. Phillips, and A. J. Drummond. 2006. “Evolution of the Human Immunodeficiency Virus Envelope Gene Is Dominated by Purifying Selection.” Genetics 174 (3): 1441–53. doi:10.1534/genetics.105.052019.
Hon, Chung-Chau, Tsan-Yuk Lam, Alexei Drummond, Andrew Rambaut, Yiu-Fai Lee, Chi-Wai Yip, Fanya Zeng, Pui-Yi Lam, Patrick T W Ng, and Frederick C C 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 (17): 8503–9. doi:10.1128/JVI.00585-06.
Drummond, Alexei J, Simon Y W Ho, Matthew J Phillips, and Andrew Rambaut. 2006. “Relaxed Phylogenetics and Dating with Confidence.” PLoS Biology 4 (5): e88. doi:10.1371/journal.pbio.0040088.
Strugnell, Jan, Jennifer Jackson, Alexei J. Drummond, and Alan Cooper. 2006. “Divergence Time Estimates for Major Cephalopod Groups: Evidence from Multiple Genes.” Cladistics 22 (1): 89–96. doi:10.1111/j.1096-0031.2006.00086.x.
Biek, Roman, Alexei J Drummond, and Mary Poss. 2006. “A Virus Reveals Population Structure and Recent Demographic History of Its Carnivore Host.” Science (New York, N.Y.) 311 (5760): 538–41. doi:10.1126/science.1121360.
Shapiro, Beth, Andrew Rambaut, and Alexei J Drummond. 2006. “Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences.” Molecular Biology and Evolution 23 (1): 7–9. doi:10.1093/molbev/msj021.
Markowitz, S., A. Drummond, K. Nieselt, and P.R. Wills. 2006. “Simulation Model of Prebiotic Evolution of Genetic Coding.” Artificial Life X: Proceedings of the Tenth International Conference on the Simulation and Synthesis of Living Systems 10: 152. http://www.sidney.com/papers/sim_prebio_alifex.pdf.
Edwards, Charles T T, Edward C Holmes, Daniel J Wilson, Raphael P Viscidi, Elaine J Abrams, Rodney E Phillips, and Alexei J Drummond. 2006. “Population Genetic Estimation of the Loss of Genetic Diversity during Horizontal Transmission of HIV-1.” BMC Evolutionary Biology 6: 28. doi:10.1186/1471-2148-6-28.

2005

Strugnell, Jan, Mark Norman, Jennifer Jackson, Alexei J Drummond, and Alan 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 (2): 426–41. doi:10.1016/j.ympev.2005.03.020.
Ho, Simon Y W, Matthew J Phillips, Alan Cooper, and Alexei J Drummond. 2005. “Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times.” Molecular Biology and Evolution 22 (7): 1561–68. doi:10.1093/molbev/msi145.
Gilbert, M.T.P., B. Shapiro, A. Drummond, and 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 (7): 1053–60. doi:10.1016/j.jas.2005.02.006.
Ho, Simon Y W, Matthew J Phillips, Alexei J Drummond, and Alan Cooper. 2005. “Accuracy of Rate Estimation Using Relaxed-Clock Models with a Critical Focus on the Early Metazoan Radiation.” Molecular Biology and Evolution 22 (5): 1355–63. doi:10.1093/molbev/msi125.
Drummond, A J, A Rambaut, B Shapiro, and O G Pybus. 2005. “Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences.” Molecular Biology and Evolution 22 (5): 1185–92. doi:10.1093/molbev/msi103.
Lunter, Gerton, István Miklós, Alexei Drummond, Jens Ledet Jensen, and Jotun Hein. 2005. “Bayesian Coestimation of Phylogeny and Sequence Alignment.” BMC Bioinformatics 6: 83. doi:10.1186/1471-2105-6-83.
Lunter, Gerton, Alexei J. Drummond, István Miklós, and Jotun Hein. 2005. “Statistical Alignment: Recent Progress, New Applications, and Challenges.” In Statistical Methods in Molecular Evolution, 375–405. New York: Springer-Verlag. http://www.springerlink.com/index/10.1007/0-387-27733-1_14.
Forsberg, Roald, Alexei J Drummond, and Jotun Hein. 2005. “Tree Measures and the Number of Segregating Sites in Time-Structured Population Samples.” BMC Genetics 6: 35. doi:10.1186/1471-2156-6-35.

2004

Shapiro, Beth, Alexei J Drummond, Andrew Rambaut, Michael C Wilson, Paul E Matheus, Andrei V Sher, Oliver G Pybus, et al. 2004. “Rise and Fall of the Beringian Steppe Bison.” Science (New York, N.Y.) 306 (5701): 1561–65. doi:10.1126/science.1101074.
Drummond, A J. 2004. “Inferring Phylogenies: An Instant Classic.” Heredity 93 (5): 519–519. doi:10.1038/sj.hdy.6800575.
Lemey, Philippe, Oliver G Pybus, Andrew Rambaut, Alexei J Drummond, David L Robertson, Pierre Roques, Michael Worobey, and Anne-Mieke Vandamme. 2004. “The Molecular Population Genetics of HIV-1 Group O.” Genetics 167 (3): 1059–68. doi:10.1534/genetics.104.026666.
Cooper, Alan, Alexei J Drummond, and Eske Willerslev. 2004. “Ancient DNA: Would the Real Neandertal Please Stand Up?” Current Biology: CB 14 (11): R431–433. doi:10.1016/j.cub.2004.05.037.
Strugnell, Jan, Mark Norman, Alexei J Drummond, and Alan Cooper. 2004. “Neotenous Origins for Pelagic Octopuses.” Current Biology: CB 14 (8): R300–301. doi:10.1016/j.cub.2004.03.048.
Goode, M., K. Strimmer, A. Drummond, E. Buckler, and A. Rodrigo. 2004. “A Brief Introduction to the Phylogenetic Analysis Library Version 1.5.” In Proceedings of the Second Conference on Asia-Pacific Bioinformatics-Volume 29, 175–79. crpit.com/confpapers/CRPITV29Goode.pdf.
Drummond, A., G.K. Nicholls, A.G. Rodrigo, and W. Solomon. 2004. “Genealogies from Time-Stamped Sequence Data.” LECTURE NOTES IN STATISTICS-NEW YORK-SPRINGER VERLAG-, 149–72. http://www.math.auckland.ac.nz/~nicholls/linkfiles/papers/ChronoGene02.pdf.

2003

Rodrigo, Allen G, Matthew Goode, Roald Forsberg, Howard A Ross, and Alexei Drummond. 2003. “Inferring Evolutionary Rates Using Serially Sampled Sequences from Several Populations.” Molecular Biology and Evolution 20 (12): 2010–18. doi:10.1093/molbev/msg215.
Bunce, Michael, Trevor H Worthy, Tom Ford, Will Hoppitt, Eske Willerslev, Alexei Drummond, and Alan Cooper. 2003. “Extreme Reversed Sexual Size Dimorphism in the Extinct New Zealand Moa Dinornis.” Nature 425 (6954): 172–75. doi:10.1038/nature01871.
Drummond, Alexei J., Oliver G. Pybus, Andrew Rambaut, Roald Forsberg, and Allen G. Rodrigo. 2003. “Measurably Evolving Populations.” Trends in Ecology & Evolution 18 (9): 481–88. doi:10.1016/S0169-5347(03)00216-7.
Biek, Roman, Allen G Rodrigo, David Holley, Alexei Drummond, Charles R Anderson Jr, Howard A Ross, and Mary Poss. 2003. “Epidemiology, Genetic Diversity, and Evolution of Endemic Feline Immunodeficiency Virus in a Population of Wild Cougars.” Journal of Virology 77 (17): 9578–89. http://www.ncbi.nlm.nih.gov/pubmed/12915571.
Pybus, O G, A J Drummond, T Nakano, B H Robertson, and A Rambaut. 2003. “The Epidemiology and Iatrogenic Transmission of Hepatitis C Virus in Egypt: A Bayesian Coalescent Approach.” Molecular Biology and Evolution 20 (3): 381–87. http://www.ncbi.nlm.nih.gov/pubmed/12644558.
Lunter, Gerton, István Miklós, Alexei Drummond, Jens Ledet Jensen, and Jotun Hein. 2003. “Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model.” In Algorithms in Bioinformatics, edited by Gary Benson and Roderic D. M. Page, 2812:228–44. Berlin, Heidelberg: Springer Berlin Heidelberg. http://www.springerlink.com/index/10.1007/978-3-540-39763-2_18.
Drummond, Alexei, Oliver G Pybus, and Andrew Rambaut. 2003. “Inference of Viral Evolutionary Rates from Molecular Sequences.” Advances in Parasitology 54: 331–58. http://www.ncbi.nlm.nih.gov/pubmed/14711090.

2002

Lambert, D. M. 2002. “Rates of Evolution in Ancient DNA from Adelie Penguins.” Science 295 (5563): 2270–73. doi:10.1126/science.1068105.
Drummond, Alexei J, Geoff K Nicholls, Allen G Rodrigo, and Wiremu Solomon. 2002. “Estimating Mutation Parameters, Population History and Genealogy Simultaneously from Temporally Spaced Sequence Data.” Genetics 161 (3): 1307–20. http://www.ncbi.nlm.nih.gov/pubmed/12136032.
Drummond, A.J. 2002. “Computational Statistical Inference for Molecular Evolution and Population Genetics”. ResearchSpace@ Auckland. http://hdl.handle.net/2292/1053.

2001

Drummond, A., and K. Strimmer. 2001. “PAL: An Object-Oriented Programming Library for Molecular Evolution and Phylogenetics.” Bioinformatics 17 (7): 662–63. doi:10.1093/bioinformatics/17.7.662.
Drummond, A., R. Forsberg, and A.G. Rodrigo. 2001. “The Inference of Stepwise Changes in Substitution Rates Using Serial Sequence Samples.” Molecular Biology and Evolution 18 (7): 1365–71. http://mbe.oxfordjournals.org/content/18/7/1365.full.

2000

Drummond, A., and A.G. Rodrigo. 2000. “Reconstructing Genealogies of Serial Samples under the Assumption of a Molecular Clock Using Serial-Sample UPGMA.” Molecular Biology and Evolution 17 (12): 1807–15. http://mbe.oxfordjournals.org/content/17/12/1807.full.