Home   Publications and Software  Research  Teaching  Industry

Picture of Alexei Dr Alexei Drummond
Senior Lecturer in Bioinformatics

Room 585, Building 303S
Department of Computer Science
University of Auckland
Private Bag 92019
Auckland, New Zealand
+64 9 3737599 ext 88298
alexei AT cs.auckland.ac.nz


Publications

Articles

  1. DRUMMOND, A.J. RAMBAUT, A. (2007) 'BEAST: Bayesian evolutionary analysis by sampling trees' BMC Evolutionary Biology, 7:214.
  2. HO S.Y.W., SHAPIRO B., PHILLIPS M.J., COOPER A., DRUMMOND A.J. 'Evidence for Time Dependency of Molecular Rate Estimates' Systematic Biology 56, 515-522, 2007 full article
  3. LEMEY P., KOSAKOVSKY POND S.L., DRUMMOND A.J., PYBUS O.G., SHAPIRO B., et al. 'Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics.' PLoS Comput Biol 3(2), e29, 2007 full article
  4. PYBUS, O.G., RAMBAUT A., BELSHAW R., FRECKLETON R.P., DRUMMOND A.J., HOLMES, E.C. 'Phylogenetic Evidence for Deleterious Mutation Load in RNA Viruses and Its Contribution to Viral Evolution' Mol Biol Evol 24, 845-852, 2007 pdf
  5. BIEK, R., DRUMMOND, A.J., POSS, M., 'A virus reveals population structure and recent demographic history of its carnivore host.' Science 311, 538-541, 2006 full article
  6. DRUMMOND, A.J., HO, S.Y.W., PHILLIPS, M.J., RAMBAUT, A., 'Relaxed phylogenetics and dating with confidence.' PLoS Biol 4, e88, 2006 full article
  7. EDWARDS, C.T.T., HOLMES, E.C., PYBUS, O.G., WILSON, D.J., VISCIDI, R.P., ABRAMS, E.J., PHILLIPS, R.E., DRUMMOND, A.J. ‘Evolution of the HIV-1 envelope gene is dominated by purifying selection’. Genetics. 174, 1441-1453. 2006 pdf
  8. EDWARDS, C.T.T., HOLMES, E.C., WILSON, D.J., VISCIDI, R.P., ABRAMS, E.J., PHILLIPS, R.E., DRUMMOND, A.J., 'Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1.' BMC Evol Biol 6, 28, 2006 full article
  9. HON, C.C., LAM, T.Y., DRUMMOND, A.J., RAMBAUT, A., LEE, Y.F., YIP, C.W., ZENG, F., LAM, P.Y., NG, P.T., LEUNG, F.C.  '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), p8503-8509, 2006 full article
  10. SHAPIRO, B., RAMBAUT, A., DRUMMOND, A.J., 'Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences.' Mol Biol Evol 23, 7-9, 2006
  11. STRUGNELL J., JACKSON J., DRUMMOND A.J., COOPER, A. ‘Divergence time estimates for major cephalopod groups: evidence from multiple genes’. Cladistics 22, 89-96, 2006 pdf
  12. DRUMMOND, A.J., RAMBAUT, A., SHAPIRO, B., PYBUS, O.G., 'Bayesian coalescent inference of past population dynamics from molecular sequences.' Mol Biol Evol 22, 1185-1192, 2005 pdf
  13. FORSBERG, R., DRUMMOND, A.J., HEIN, J., 'Tree measures and the number of segregating sites in time-structured population samples.' BMC Genet 6, 35, 2005 full article
  14. GILBERT, M.T.P., SHAPIRO, B., DRUMMOND, A., COOPER, A. ‘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, 2005
  15. HO, S.Y.W., PHILLIPS, M.J., COOPER, A., DRUMMOND, A.J., 'Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.' Mol Biol Evol 22, 1561-1568, 2005 pdf
  16. HO, S.Y.W., PHILLIPS, M.J., DRUMMOND, A.J., COOPER, A., 'Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation.' Mol Biol Evol 22, 1355-1363, 2005 pdf
  17. LUNTER, G., MIKLÓS, I., DRUMMOND, A., JENSEN, J.L., HEIN, J., 'Bayesian coestimation of phylogeny and sequence alignment.' BMC Bioinformatics 6, 83, 2005 full article
  18. STRUGNELL, J., NORMAN, M., JACKSON, J., DRUMMOND, A.J., COOPER, A., 'Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework.' Mol Phylogenet Evol 37, 426-441, 2005
  19. COOPER, A., DRUMMOND, A.J., WILLERSLEV, E., 'Ancient DNA: would the real Neandertal please stand up?' Curr Biol 14, R431-433, 2004
  20. LEMEY, P., PYBUS, O.G., RAMBAUT, A., DRUMMOND, A.J., ROBERTSON, D.L., ROQUES, P., WOROBEY, M., VANDAMME, A.-M., 'The molecular population genetics of HIV-1 group O.' Genetics 167, 1059-1068, 2004
  21. SHAPIRO, B., DRUMMOND, A.J., RAMBAUT, A., WILSON, M.C., MATHEUS, P.E., SHER, A.V., PYBUS, O.G., GILBERT, M.T.P., BARNES, I., BINLADEN, J., WILLERSLEV, E., HANSEN, A.J., BARYSHNIKOV, G.F., BURNS, J.A., DAVYDOV, S., DRIVER, J.C., FROESE, D.G., HARINGTON, C.R., KEDDIE, G., KOSINTSEV, P., KUNZ, M.L., MARTIN, L.D., STEPHENSON, R.O., STORER, J., TEDFORD, R., ZIMOV, S., COOPER, A., 'Rise and fall of the Beringian steppe bison.' Science 306, 1561-1565, 2004 pdf
  22. STRUGNELL, J., NORMAN, M., DRUMMOND, A.J., COOPER, A., 'Neotenous origins for pelagic octopuses.' Curr Biol 14, R300-301, 2004 pdf
  23. BIEK, R., RODRIGO, A.G.2, HOLLEY, D., DRUMMOND, A., ANDERSON, C.R., ROSS, H.A.2, POSS, M., 'Epidemiology, genetic diversity, and evolution of endemic feline immunodeficiency virus in a population of wild cougars.' J Virol 77, 9578-9589, 2003 full article
  24. BUNCE, M., WORTHY, T.H., FORD, T., HOPPITT, W., WILLERSLEV, E., DRUMMOND, A., COOPER, A., 'Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis.' Nature 425, 172-175, 2003 pdf
  25. DRUMMOND, A.J., PYBUS, O.G., RAMBAUT, A., FORSBERG, R., RODRIGO A.G. ‘Measurably evolving populations’. Trends Ecol Evol 18, 481-488, 2003
  26. LUNTER, G.A., MIKLÓS, I., JENSEN, J.L., DRUMMOND, A., HEIN, J. ‘Bayesian phylogenetic inference under a statistical insertion-deletion model.’ Lecture Notes in Bioinformatics 2812, 228-244, 2003
  27. PYBUS, O.G., DRUMMOND, A.J., NAKANO, T., ROBERTSON, B.H., RAMBAUT, A., 'The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach.' Mol Biol Evol 20, 381-387, 2003 pdf
  28. RODRIGO, A.G., GOODE, M., FORSBERG, R., ROSS, H.A., DRUMMOND, A., 'Inferring evolutionary rates using serially sampled sequences from several populations.' Mol Biol Evol 20, 2010-2018, 2003 pdf
  29. DRUMMOND, A., PYBUS, O.G., RAMBAUT, A., 'Inference of viral evolutionary rates from molecular sequences.' Adv Parasitol 54, 331-358, 2002
  30. DRUMMOND, A.J., NICHOLLS, G.K., RODRIGO, A.G., SOLOMON, W., 'Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data.' Genetics 161, 1307-1320, 2002 pdf -- over 100 citations
  31. LAMBERT, D.M., RITCHIE, P.A., MILLAR, C.D., HOLLAND, B., DRUMMOND, A.J., BARONI, C., 'Rates of evolution in ancient DNA from Adélie penguins.' Science 295, 2270-2273, 2002 pdf
  32. DRUMMOND, A., FORSBERG, R., RODRIGO, A.G. 2, 'The inference of stepwise changes in substitution rates using serial sequence samples.' Mol Biol Evol 18, 1365-1371, 2001
  33. DRUMMOND, A., STRIMMER, K., 'PAL: an object-oriented programming library for molecular evolution and phylogenetics.' Bioinformatics 17, 662-663, 2001 pdf
  34. DRUMMOND, A., RODRIGO, A.G., 'Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA.' Mol Biol Evol 17, 1807-1815, 2000 pdf

Book Sections

  1. DRUMMOND, A.J., NICHOLLS, G.K., RODRIGO, A.G., SOLOMON, W. 'Genealogies from time-stamped  sequence data', in  'Tools for Constructing Chronologies', Eds. C Buck and A. Millard. Springer, 151-174, 2003
  2. LUNTER, G.A., DRUMMOND, A.J., MIKLÓS, I., HEIN, J. 'Statistical Alignment: Recent Progress, New Applications and Challenges', in 'Statistical Methods in Molecular Evolution', Rasmus Nielsen, Editor. Springer 2005
  3. HOLMES, E.C., DRUMMOND A.J. 'The evolutionary genetics of viral emergence', in 'Wildlife and Emerging Zoonotic Diseases: The Biology, Circumstances, and Consequences of Cross-Species Transmission' J. Mackenzie, Editor. Curr Top Micro Immunol 315 Springer-Verlag, 51-66, 2007
  4. RODRIGO, A., EWING, G. DRUMMOND, A.J. 'The evolutionary analysis of measurably evolving populations using serially sampled gene sequences', in 'Reconstructing Evolution: New Mathematical and Computational Advances', Edited by Olivier Gascuel and Mike Steel. Oxford University Press 2007
  5. DRUMMOND, A.J., HOSKING, J., LUTTEROTH, C., WEBER, G., WUENSCHE, B. 'Computing Away Climate Change', in 'Carbon Neutral by 2020: How New Zealanders can tackle climate change', Edited by Niki Harre and Quentin D Atkinson. Craig Potton Publishing 2007

Commentary

  1. DRUMMOND, A.J. ‘Inferring Phylogenies – an instant classic’. Heredity 93, 519, 2004
  2. YANG, Z.H., STEPHENS, D., DAWSON, K.J., DRUMMOND, A., NICHOLLS, G.K., GRIFFITHS, R.C., WILKINSON-HERBOTS, H.M., BEAUMONT, M.A., BAIRD, S.J.E., LASCOUX, M., LEBLOIS, R., ESTOUP, A., NIELSEN, R., HEY, J., STUMPF, M.P.H. ‘Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities – Discussion’. J Roy Stat Soc A 166, 188-201, 2003

Conference Proceedings

  1. MARKOWITZ, S.5, DRUMMOND, A., NIESELT, K., WILLS, P.R. 'Simulation Model of Prebiotic Evolution of Genetic Coding', in ALife X, the tenth annual conference on the simulation and synthesis of living systems, June 2006.
  2. GOODE, M., K. STRIMMER, A. DRUMMOND, E. BUCKLER, AND A. RODRIGO. 'A brief introduction to the phylogenetic analysis library, version 1.5', in 'Proceedings of the Second Asia-Pacifica Bioinformatics Conference (APBC2004)', Y-P Phoebe Chen, Editor. Dunedin, NZ, January 2004. (Publisher: CRPIT).

Software

  1. Geneious - search, filter and organize molecular sequence data as well as performing sequence alignment and quick phylogenetic tree building (with Biomatters).
  2. BEAST - Bayesian evolutionary analysis sampling trees (with Andrew Rambaut)
  3. PAL - Phylogenetics analysis library (with many co-authors)


Last modified: November 5, 2007