Publications

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BEAST Documentation->Publications

Some recent publications that use BEAST: (by year then alphabetical). This is not comprehensive but demonstrates the range of applications for which BEAST is being used. We would like to encourage people to add their publications here and, if possible, upload or link to their XML files.

2009-present
We are pleased to say that the number of publications citing BEAST has now reached >1000 and therefore we are no longer able to keep this list up-to-date.
2008
  1. Atkinson QD, Gray RD & Drummond AJ (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.
  2. Baillie GJ, Kolokotronis SO, Waltari E, Maffei JG, Kramer LD, Perkins SL (2008) Phylogenetic and evolutionary analyses of St. Louis encephalitis virus genomes. Molecular Phylogenetics and Evolution 47, 717-728. Abstract PDF
  3. Berendzen PB, Gamble T, Simons AM (2008) Phylogeography of the bigeye chub, Hybopsis amblops (Teleostei: Cypriniformes): Early Pleistocene diversification and post-glacial range expansion. Journal of Fish Biology 73, 2021-2039. Abstract
  4. Brown JW, Rest JS, García-Moreno J, Sorenson MD, & Mindell DP (2008) Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages. BMC Biology 6, 6. Full text
  5. Cutter AD (2008) Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Molecular Biology and Evolution 25, 778-786.
  6. Duffy S, Shackelton LA, Holmes EC (2008) Rates of evolutionary change in viruses: patterns and determinants. Nature Review Genetics 9, 267-276.
  7. Endicott P, Ho SYW (2008) A Bayesian evaluation of human mitochondrial substitution rates. American Journal of Human Genetics 82, 895-902.
  8. Fagundes NJR, Kanitz R, Eckert R, Valls ACS, Bogo MR, Salzano FM, Smith DG, Silva-Jr W, Zago MA, Ribeiro-dos-Santos AK, Santos SEB, Petzl-Erler ML & Bonatto SL (2008) Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas. American Journal of Human Genetics 82, 583-592. Abstract
  9. Hao DC, Xiao PG, Huang B, Ge G, Yang L (2008) Interspecific relationships and origins of Taxaceae and Cephalotaxaceae revealed by partitioned Bayesian analyses of chloroplast and nuclear DNA sequences Plant Systematics and Evolution DOI 10.1007/s00606-008-0069-0
  10. Hay JM, Subramanian S, Millar CD, Mohandesan E & Lambert DM (2008) Rapid molecular evolution in a living fossil. Trends in Genetics 24, 106-109.
  11. Heller, R, Lorenzen ED, Okello JBA, Masembe C, Siegismund HR (2008) Mid-Holocene decline in African buffalos inferred from Bayesian coalescent-based analyses of microsatellites and mitochondrial DNA. Molecular Ecology 17, 4845-4858. Abstract
  12. Kitchen A, Miyamoto MM & Mulligan CJ (2008) A Three-Stage Colonization Model for the Peopling of the Americas. PLoS ONE 3, e1596. Full Text
  13. Koscinski D, Handford P, Tubaro PL, et al. (2008) Pleistocene climatic cycling and diversification of the Andean treefrog, Hypsiboas andinus. Molecular Ecology 17, 2012-2025.
  14. Krause J, Unger T, Noçon A, Malaspinas AS, Kolokotronis SO, Stiller M, Soibelzon L, Spriggs H, Dear PH, Briggs AH, Bray SE, O'Brien SJ, Rabeder G, Matheus P, Cooper A, Slatkin M, Pääbo S, Hofreiter M (2008) Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evolutionary Biology 8, 220. Full text
  15. Leschen RAB, Buckley TR, Harman HM, Shulmeister J (2008) Determining the origin and age of the Westland beech (Nothofagus) gap, New Zealand, using fungus beetle genetics. Molecular Ecology 17, 1256–1276
  16. Paape T, Igic B, Smith SD, et al. (2008) A 15-Myr-old genetic bottleneck. Molecular Biology and Evolution 25, 655-663.
  17. Phillimore AB, Price TD (2008) Density-dependent cladogenesis in birds. PLoS Biology 6(3): e71
  18. Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK & Holmes EC (2008) The Genomic and Epidemiological Dynamics of Human Influenza A Virus. Nature 453, 615-619. Abstract PDF
  19. Ruzzante DE, Walde SJ, Gosse JC, Cussac VE, Habit E, Zemlak TS & Adams EDM (2008) Climate control on ancestral population dynamics: insight from Patagonian fish phylogeography. Molecular Ecology 17, 2234-2244.
  20. Schultz TR, Brady SG (2008) Major evolutionary transitions in ant agriculture. PNAS 105, 5435-5440.
  21. Tee KK, Pybus OG, Liao H, Uenishi R, Hase S, Kamarulzaman A, Li XJ, Takebe Y (2008) Chronology of the HIV-1 CRF07_BC expansion in East Asia. AIDS 22, 156-158.
  22. Tee KK, Pybus OG, Li XJ, Han X, Shang H, Kamarulzaman A, Takebe Y (2008) Temporal and spatial dynamics of human immunodeficiency virus type 1 circulating recombinant forms 08_BC and 07_BC in Asia. Journal of Virology 82, 9206-9215.
2007
  1. Aulicino PC, Holmes EC, Rocco C, Mangano A, Sen L (2007) Extremely rapid spread of human immunodeficiency virus type 1 BF recombinants in Argentina. Journal of Virology 81, 427-429.
  2. Barnes I, Shapiro B, Lister A, Kuznetsova T, Sher A, Guthrie D, Thomas MG (2007) Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Current Biology 17, 1072-1075.
  3. Bello G, Eyer-Silva WA, Couto-Fernandez JC, Guimaraes ML, Chequer-Fernandez SL, Teixeira SL, Morgado MG (2007) Demographic history of HIV-1 subtypes B and F in Brazil. Infection, Genetics and Evolution 7, 263-270.
  4. Bertolotti L, Kitron U and Goldberg TL (2007) Diversity and evolution of West Nile virus in Illinois and the United States, 2002-2005. Virology 360, 143-149.
  5. Biek R (2007) Evolutionary dynamics and spatial genetic structure of epizootic hemorrhagic disease virus in the eastern United States. Infection, Genetics and Evolution 7, 651-655.
  6. Biek R, Henderson JC, Waller LA, Rupprecht CE, Real LA (2007) A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus. PNAS 104, 7993-7998.
  7. Bird BH, Khristova ML, Rollin PE, Ksiazek TG, Nichol ST (2007) Complete genome analysis of 33 ecologically and biologically diverse rift valley fever virus strains reveals widespread virus movement and low genetic diversity due to recent common ancestry. Journal of Virology 81, 2805-2816.
  8. Bryant JE, Holmes EC, Barrett ADT (2007) Out of Africa: A molecular perspective on the introduction of yellow fever virus into the Americas. PLoS Pathogens 3, 668-673.
  9. David D, Hughes GJ, Yakobson BA, Davidson I, Un H, Aylan O, Kuzmin IV, Rupprecht CE (2007) Identification of novel canine rabies virus clades in the Middle East and North Africa. Journal of General Virology 88, 967-980.
  10. Dixon CJ, Schonswetter P, Schneeweiss GM (2007) Traces of ancient range shifts in a mountain plant group (Androsace halleri complex, Primulaceae). Molecular Ecology 16, 3890-3901.
  11. Ducatez MF, Olinger CM, Owoade AA, Tarnagda Z, Tahita MC, Sow A, De Landtsheer S, Ammerlaan W, Ouedraogo JB, Osterhaus ADME, Fouchier RAM, Muller CP (2007) Molecular and antigenic evolution and geographical spread of H5N1 highly pathogenic avian influenza viruses in western Africa. J Gen Virol 88, 2297-2306.
  12. Edwards CJ, Bollongino R, Scheu A, Chamberlain A, Tresset A, Vigne J-D, Baird JF, Larson G, Ho SYW, Heupink TH, Shapiro B et al (2007) Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Proc R Soc B 274, 1377-1385.
  13. Emerson BC (2007) Alarm bells for the molecular clock? No support for Ho et al.'s model of time-dependent molecular rate estimates. Systematic Biology 56, 337-345.
  14. Eyer-Silva WA, Bello G, Morgado MG (2007) Molecular evidence that human immunodeficiency virus type 1 dissemination in a small Brazilian city was already taking place in the early 1990s Memorias do Instituto Oswaldo Cruz 102, 647-649.
  15. Finlay EK, Gaillard C, Vahidi SM, Mirhoseini SZ, Jianlin H, Qi XB, El-Barody MA, Baird JF, Healy BC, Bradley DG. (2007) Bayesian inference of population expansions in domestic bovines. Biology Letters 3, 449-52. Full Text
  16. Gomez-Valero L, Silva FJ, Simon JC, Latorre A (2007) Genome reduction of the aphid endosymbiont Buchnera aphidicola in a recent evolutionary time scale. Gene 389, 87-95.
  17. Gottschling M, Stamatakis A, Nindl I, Stockfleth E, Alonso A, and Bravo IG (2007) Multiple evolutionary mechanisms drive papillomavirus diversification. Molecular Biology and Evolution 24, 1242-1258.
  18. Ho SYW, Heupink TH, Rambaut A, Shapiro B (2007) Bayesian estimation of sequence damage in ancient DNA. Molecular Biology and Evolution 24, 1416-1422.
  19. Ho SYW, Kolokotronis SO, Allaby RG (2007) Elevated substitution rates estimated from ancient DNA sequences. Biology Letters 3, 702-705.
  20. Ho SYW, Shapiro B, Phillips MJ, Cooper A, Drummond AJ (2007) Evidence for Time Dependency of Molecular Rate Estimates. Systematic Biology 56, 515-522.
  21. Hurtado LA, Frey M, Gaube P, Pfeiler E, Markow TA (2007) Geographical subdivision, demographic history and gene flow in two sympatric species of intertidal snails, Nerita scabricosta and Nerita funiculata, from the tropical eastern Pacific. Marine Biology 151, 1863-1873.
  22. Lembo T, Haydon DT, Velasco-Villa A, Rupprecht CE, Packer C, Brandao PE, Kuzmin IV, Fooks AR, Barrat J, Cleaveland S (2007) Molecular epidemiology identifies only a single rabies virus variant circulating in complex carnivore communities of the Serengeti. Proc Roy Soc B 274, 2123-2130.
  23. Lemey P, Kosakovsky Pond SL, Drummond AJ, Pybus, OG, Shapiro B, Barroso H, Taveira N and Rambaut A (2007) Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Computational Biology 3, 282-292.
  24. Li Y, Carroll DS, Gardner SN, Walsh MC, Vitalis EA, Damon IK (2007) On the origin of smallpox: Correlating variola phylogenics with historical smallpox records. PNAS 104, 15787-15792.
  25. Loader SP, Pisani D, Cotton JA, Gower DJ, Day JJ, Wilkinson M (2007) Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians. Biology Letters 3, 505-508.
  26. Martínez-Solano I., Jockusch EL, Wake DB (2007) Extreme population subdivision throughout a continuous range: phylogeography of Batrachoseps attenuatus (Caudata: Plethodontidae) in western North America. Molecular Ecology 16, 4335-4355.
  27. Melo M, O'Ryan C (2007) Genetic differentiation between Principe Island and mainland populations of the grey parrot (Psittacus erithacus), and implications for conservation. Molecular Ecology 16, 1673-1685.
  28. Moore, B.R., and M.J. Donoghue (2007) Correlates of diversification in the plant clade Dipsacales: Geographic movement and evolutionary innovation. American Naturalist 170, S28-S55.
  29. Njouom R, Nerrienet E, Dubois M, Lachenal G, Rousset D, Vessiere A, Ayouba A, Pasquier C, Pouillot R (2007) The hepatitis C virus epidemic in Cameroon: genetic evidence for rapid transmission between 1920 and 1960. Infection, Genetics and Evolution 7, 361-367.
  30. Paraskevis D, Magiorkinis E, Magiorkinis G, Sypsa V, Paparizos V, Lazanas M, Gargalianos P, Antoniadou A, Panos G, Chrysos G, Sambatakou H, Karafoulidou A, Skoutelis A, Kordossis T, Koratzanis G, Theodoridou M, Daikos GL, Nikolopoulos G, Pybus OG, Hatzakis A (2007) Increasing prevalence of HIV-1 subtype a in Greece: Estimating epidemic history and origin. Journal of Infectious Diseases 196, 1167-1176.
  31. Pereira CAD, Leal ES, Durigon EL (2007) Selective regimen shift and demographic growth increase associated with the emergence of high-fitness variants of canine parvovirus. Infection, Genetics and Evolution 7, 399-409.
  32. Perez-Losada M, Crandall KA, Zenilman J and Viscidi RP (2007) Temporal trends in gonococcal population genetics in a high prevalence urban community. Infection, Genetics and Evolution 7, 271-278.
  33. Porter ML, Dittmar K, Perez-Losada M (2007) How long does evolution of the troglomorphic form take? Estimating divergence times in Astyanax mexicanus. Acta Carsologica 36, 173-182
  34. Rector A, Lemey P, Tachezy R, Mostmans S, Ghim SJ, Van Doorslaer K, Roelke M, Bush M, Montali RJ, Joslin J, Burk RD, Jenson AB, Sundberg JP, Shapiro B, Van Ranst M (2007) Ancient papillomavirus-host co-speciation in Felidae. Genome Biology 8, R57.
  35. Saarma U, Ho SYW, Pybus OG, Kaljuste M, Tumanov IL, Kojola I, Vorobiev AA, Markov NI, Saveljev AP, Valdmann H, Lyapunova EA, Abramov AV, Mannil P, Korsten M, Vulla E, Pazetnov SV, Pazetnov VS, Putchkovskiy SV, Rokov AM (2007) Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages. Molecular Ecology 16, 401-413. XML
  36. Sanders KL, Lee MSY (2007) Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds. Biology Letters 3, 275-279.
  37. Snapinn KW, Holmes EC, Young DS, Bernard KA, Kramer LD and Ebel GD (2007) Declining growth rate of West Nile virus in North America. Journal of Virology 81, 2531-2534.
  38. Vijaykrishna D, Smith GJD, Zhang JX, Peiris JSM, Chen H, Guan Y (2007) Evolutionary insights into the ecology of coronaviruses. Journal of Virology 81, 4012-4020.
  39. Vosloo W, de Klerk LM, Boshoff CI, Botha B, Dwarka RM, Keet D, Haydon DT (2007) Characterisation of a SAT-1 outbreak of foot-and-mouth disease in captive African buffalo (Syncerus caffer): clinical symptoms, genetic characterisation and phylogenetic comparison of outbreak isolate. Veterinary Microbiology 120, 226-240.
  40. Zhou Y, Holmes EC (2007) Bayesian estimates of the evolutionary rate and age of hepatitis B virus. Journal of Molecular Evolution 65, 197-205.
2006
  1. Atarhouch T, Ruber L, Gonzalez EG, Albert EM, Rami M, Dakkak A, Zardoya R (2006) Signature of an early genetic bottleneck in a population of Moroccan sardines (Sardina pilchardus). Molecular Phylogenetics and Evolution 39(2): 373-383
  2. Biek R, Drummond AJ, and Poss M (2006) A virus reveals population structure and recent demographic history of its carnivore host. Science 311: 538-541
  3. Bohonak AJ, Holland MD, Santer B, Zeller M, Kearns CM, Hairston, Jr. NJ (2006) The population genetic consequences of diapause in Eudiaptomus copepods. Arch. Hydrobiol. 167: 183-202
  4. Calattini S, Chevalier SA, Duprez R, Afonso P, Froment A, Gessain A, Mahieux R (2006) Human T-cell lymphotropic virus type 3: Complete nucleotide sequence and characterization of the human Tax3 protein. Journal of Virology 80(19):9876-9888 Full Text
  5. Chen R and Holmes EC (2006) Avian Influenza Virus Exhibits Rapid Evolutionary Dynamics. Mol Biol Evol 23: 2336-2341
  6. Cottam EM, Haydon DT, Paton DJ, Gloster J, Wilesmith JW, Ferris NP, Hutchings GH, King DP (2006) Molecular epidemiology of the foot-and-mouth disease virus outbreak in the United Kingdom in 2001. Journal of Virology 80(22): 11274-11282 Full Text
  7. Davis LA, Roalson EH, Cornell KL, McClanahan KD, Webster MS (2006) Genetic divergence and migration patterns in a North American passerine bird: implications for evolution and conservation. Molecular Ecology 15 (8): 2141-2152
  8. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed Phylogenetics and Dating with Confidence. PLoS Biol 4 (5): e88 Full Text
  9. Edwards CTT, Holmes EC, Wilson DJ, Viscidi RP, Abrams EJ, Phillips RE, Drummond AJ (2006) Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1. BMC Evolutionary Biology 6: 28 Full Text
  10. Edwards CTT, Holmes EC, Pybus OG, Wilson DJ, Viscidi RP, Abrams EJ, Phillips RE, Drummond AJ (2006) Evolution of the HIV-1 envelope gene is dominated by purifying selection. Genetics 174, 1441-1453
  11. Eppinger M, Baar C, Linz B, Raddatz G, Lanz C, Keller H, Morelli G, Gressmann H, Achtman M, Schuster SC (2006) Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines.PLoS Genetics 2(7): e120
  12. Grazziontin FG, Monzel M, Echeverrigaray S, Bonatto SL (2006) Phylogeography of the Bothrops jararaca complex (Serpentes: Viperidae): past fragmentation and island colonization in the Brazilian Atlantic Forest. Molecular Ecology 15 3969-3982
  13. Guo SC, Savolainen P, Su JP, Zhang Q, Qi DL, Zhou J, Zhong Y, Zhao XQ, Liu JQ (2006) Origin of mitochondrial DNA diversity of domestic yaks. BMC Evolutionary Biology 6 73 Full Text
  14. Harlin-Cognato A, Bickham JW, Loughlin TR, Honeycutt RL (2006) Glacial refugia and the phylogeography of Steller's sea lion (Eumatopias jubatus) in the North Pacific. Journal of Evolutionary Biology 19 (3): 955-969
  15. Hayward A & Stone GN (2006) Comparative phylogeography across two trophic levels: the oak gall wasp Andricus kollari and its chalcid parasitoid Megastigmus stigmatizans. Molecular Ecology 15: 479–489
  16. Hon CC, Lam TY, Drummond A, Rambaut A, Lee YF, Yip CW, Zeng FY, Lam PY, Ng PTW, Leung FCC (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): 8503-8509 Full Text
  17. Jones WJ, Won Y-J, Maas PAY, Smith PJ, Lutz RA, Vrijenhoek RC (2006) Evolution of habitat use by deep-sea mussels. Marine Biology 148, 841-851
  18. Martinez-Solano I, Teixeira J, Buckley D, Garcia-Paris M (2006) Mitochondrial DNA phylogeography of Lissotriton boscai (Caudata, Salamandridae): evidence for old, multiple refugia in an Iberian endemic. Molecular Ecology 15(11): 3375-3388
  19. Nakano T, Lu L, He Y, Fu Y, Robertson BH, Pybus OG (2006) Population genetic history of hepatitis C virus 1b infection in China. J Gen Virol 87: 73-82
  20. de Oliveira T, Pybus OG, Rambaut A, Salemi M, Cassol S, Ciccozzi M, Rezza G, Gattinara GC, D'Arrigo R, Amicosante M, Perrin L, Colizzi V & Perno CF (2006) Molecular Epidemiology, HIV-1 and HCV sequences from Libyan outbreak. Nature 444, advanced online publication Full Text.
  21. Pyrc K, Dijkman R, Deng L, Jebbink MF, Ross HA, Berkhout B, Van der Hoek L (2006) Mosaic structure of human coronavirus NL63, one thousand years of evolution. Journal of Molecular Biology 364(5): 964-973
  22. Raterman D, Meredith RW, Ruedas LA, Springer MS (2006) Phylogenetic relationships of the cuscuses and brushtail possums (Marsupialia : Phalangeridae) using the nuclear gene BRCA1. Australian Journal of Zoology 54:353-361
  23. Rogaev EI, Moliaka YK, Malyarchuk BA, Kondrashov FA, Derenko MV, et al. (2006) Complete Mitochondrial Genome and Phylogeny of Pleistocene Mammoth Mammuthus primigenius. PLoS Biol 4(3): e73 Full Text
  24. Roumagnac P, Weill FX, Dolecek C, Baker S, Brisse S, Chinh NT, Le TAH, Acosta CJ, Farrar J, Dougan G, Achtman M. (2006) Evolutionary history of Salmonella Typhi. Science 314: 1301-1304
  25. Sachet JM, Roques A, Despres L (2006) Linking patterns and processes of species diversification in the cone flies Strobilomyia (Diptera : Anthomylidae). Molecular Phylogenetics and Evlution 41(3); 606-621
  26. Shackelton LA, Holmes EC (2006) Phylogenetic evidence for the rapid evolution of human B19 erythrovirus. Journal of Virology 80(7): 3666-3669 Full Text
  27. Shackelton LA, Rambaut A, Pybus OG, Holmes EC (2006) JC virus evolution and its association with human populations. Journal of Virology 80(20): 9928-9933 Full Text
  28. Verbeeck J, Maes P, Lemey P, Pybus OG, Wollants E, Song E, Nevens F, Fevery J, Delport W, Van der Merwe S, Van Ranst M (2006) Investigating the origin and spread of hepatitis C virus genotype 5a. Journal of Virology 80 (9): 4220-4226
  29. Vijgen L, Keyaerts E, Lemey P, Maes P, Van Reeth K, Nauwynck H, Pensaert M, Van Ranst M (2006) Evolutionary history of the closely related group 2 coronaviruses: Porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus OC43. Journal of Virology 80 (14): 7270-7274 Full Text
  30. Wrobel B, Torres-Puente M, Jimenez N, Bracho MA, Garcia-Robles I, Moya A, Gonzalez-Candelas F (2006) Analysis of the overdispersed clock in the short-term evolution of hepatitis C virus: Using the E1/E2 gene sequences to infer infection dates in a single source outbreak. Molecular Biology and Evolution 23: 1242-1253
2005
  1. Carrington CVF, Foster JE, Pybus OG, Bennett SN, Holmes EC (2005) Invasion and Maintenance of Dengue Virus Type 2 and Type 4 in the Americas. J Virol 79: 14680-14687
  2. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 22 (5):1185-92
  3. Ho SY, Phillips MJ, Drummond AJ, Cooper A. 2005. Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Mol Biol Evol. 22 (5):1355-63.
  4. Ho SY, Phillips MJ, Cooper A, Drummond AJ. 2005. Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times. Mol Biol Evol 22 (7):1561-156.
  5. Hue S, Pillay D, Clewley JP, Pybus OG (2005) Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups PNAS 102 (12): 4425-4429 Full Text
  6. Hughes GJ, Orciari LA, Rupprecht CE (2005) Evolutionary timescale of rabies virus adaptation to North American bats inferred from the substitution rate of the nucleoprotein gene. Journal of General Virology 86: 1467-1474
  7. Lunter G, Miklos I, Drummond A, Jensen JL, Hein J. 2005. Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics 6 (1):83.
  8. Shackelton LA, Holmes EC (2005) Phylogenetic Evidence for the Rapid Evolution of Human B19 Erythrovirus. J Virol 80: 3666-3669
  9. Verovnik R, Sket B, Trontelj P (2005) The colonization of Europe by the freshwater crustacean Asellus aquaticus (Crustacea : Isopoda) proceeded from ancient refugia and was directed by habitat connectivity. Molecular Ecology 14 (14): 4355-4369
  10. Vijgen L, Keyaerts E, Lemey P, Moes E, Li S, Vandamme AM, Van Ranst M (2005) Circulation of genetically distinct contemporary human coronavirus OC43 strains. Virology 337 (1): 85-92
  11. Walsh PD, Biek R, Real LA. 2005. Wave-like spread of Ebola Zaire. PLoS Biology 3 (11). Full Text
  12. Weinstock J, Willerslev E, Sher A, Tong WF, Ho SYW, Rubenstein D, Storer J, Burns J, Martin L, Bravi C, Prieto A, Froese D, Scott E, Lai XL, Cooper A (2005) Evolution, systematics, and phylogeography of Pleistocene horses in the New World: A molecular perspective. PLoS Biology 3 (8): 1373-1379 Full Text
2004
  1. Achaz, G., S. Palmer, M. Kearney, F. Maldarelli, J. W. Mellors, J. M. Coffin and J. Wakeley. 2004. A Robust Measure of HIV-1 Population Turnover Within Chronically Infected Individuals. Mol Biol Evol 21:1902-1912. Full Text
  2. Henk C. den Bakker, G. C. Zuccarello, TH. W. Kuyper and M. E. Noordeloos. 2004. Evolution and host specificity in the ectomycorrhizal genus Leccinum. New Phytologist 163: 201. Full Text
  3. Hughes, G.J., A. Páez, J. Bóshell, C.E. Rupprecht. 2004. A phylogenetic reconstruction of the epidemiological history of canine rabies virus variants in Colombia. Infection, Genetics and Evolution. 4:45-51. PubMed
  4. Lemey P, Pybus OG, Rambaut A, Drummond A, Roques P, Worobey M & Vandamme A-M (2004) The molecular population genetics of HIV-1 group O. Genetics. 167: 1059-1068. Full Text, PubMed, XML
  5. Paraskevis D, Magiorkinis E, Magiorkinis G, Kiosses VG, Lemey P, Vandamme A-M, Rambaut A, Hatzakis A (2004) Phylogenetic Reconstruction of a Known HIV-1 CRF04cpx Transmission Network Using Maximum Likelihood and Bayesian Methods. Journal of Molecular Evolution 59, 709-717
  6. Shapiro B, Drummond AJ, Rambaut A, et al. (2004) Rise and fall of the Beringian steppe bison. Science 306, 1561-1565.. Full Text, PubMed, XML
2003
  1. Bunce, M., T.H. Worthy, T. Ford, W. Hoppitt, E. Willeslev, A. Drummond & A. Cooper. 2003. Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 425: 172-175. PubMed
  2. Drummond, A.J., O.G. Pybus, A. Rambaut, R. Forsberg & A.G. Rodrigo. 2003. Measurably evolving populations. Trends Ecol Evol 18: 481-488.
  3. Drummond, A., O.G. Pybus & A. Rambaut (2003) Inference of viral evolutionary rates from molecular sequences. Advances In Parasitology 54: 331-358. PubMed
  4. Lunter, G.A., I. Miklós, J.L. Jensen, A. Drummond, J. Hein. 2003. Bayesian Phylogenetic Inference under a Statistical Insertion-Deletion Model. Lecture Notes in Bioinformatics 2812:228-244.
  5. Pybus, O.G., A.J. Drummond, T. Nakano, B.H. Robertson & A. Rambaut. 2003. The epidemiology and iatrogenic transmission of hepatitis C virus in egypt: a bayesian coalescent approach. Mol Biol Evol 20: 381-7. Full Text, PubMed

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