Publications

Virus and Pathogen Evolution

Phylogeography takes a relaxed random walk in continuous space and time.: Lemey P, Rambaut A, Welch JJ & Suchard MA (2010) Mol Biol Evol In press

Recent human to poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus.: Lowder BV, Guinane CM, Zakour NLB, Weinert L, Conway-Morris A, Cartwright RA, Simpson AJ, Rambaut A, N�bel U, & Fitzgerald JR (2009) PNAS doi: 10.1073/pnas.0909285106

Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom.: Hughes GJ, Fearnhill E, Dunn D, Lycett SJ, Rambaut A & Leigh Brown AJ (2009) PLoS Pathogens 5, e1000590.

Making Privileged Data Public: Influenza - Response.: Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, Jombart T, Hinsley WR, Grassly NC, Balloux F, Ghani AC, Rambaut A & Ferguson NM (2009) Science 325, 1072 - 1073.

Bayesian Phylogeography Finds Its Roots.: Lemey P, Rambaut A, Drummond AJ & Suchard MA (2009) PLoS Comput Biol 5, e1000520.

Evolutionary analysis of the dynamics of viral infectious disease.: Pybus OG & Rambaut A (2009) Nature Reviews Genetics 10, 540-550.

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.: Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JSM, Guan Y & Rambaut A (2009) Nature 459, 1122-1125.

Pandemic Potential of a Strain of Influenza A (H1N1) : Early Findings.: Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, Jombart T, Hinsley WR, Grassly NC, Balloux F, Ghani AC, Ferguson NM, Rambaut A, Pybus OG, Lopez-Gatell H, Apluche-Aranda CM, Chapela IB, Zavala EP, Guevara DME, Checchi E, Garcia E, Hugonnet S, Roth C & and The WHO Rapid Pandemic Assessment Collaboration. 2009. (2009) Science 324, 1557-1561.

The RNA Virus Database.: Belshaw R, de Oliveira T, Markowitz S & Rambaut A (2009) Nucleic Acids Research 37, D431-D435.

Conserved footprints of APOBEC3G on hypermutated HIV-1 and HERV-K(HML2) sequences.: Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A & Iversen AKN (2008) J Virol 82, 8743-8761.

Complete list for: Virus and Pathogen Evolution

Molecular Evolution and Phylogenetic Analyses

A generation time effect on the rate of molecular evolution in invertebrates.: Thomas JA, Welch JJ, Lanfear R & Bromham L (2010) Mol Biol Evol In press

Quantifying adaptive evolution in the Drosophila immune system: a high throughput approach.: Obbard DJ, Welch JJ, Kim K-W & Jiggins FM (2009) PLoS Genetics 5, e1000698.

Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally.: Weinert, LA, Welch JJ & Jiggins FM (2009) Proc Roy Soc B 276, 3619-3627.

Inferring selection in the Anopheles gambiae species complex: an example from immune-related serine protease inhibitors.: Obbard DJ, Welch JJ & Little TJ (2009) Malaria Journal 8, 117.

Many-Core Algorithms for Statistical Phylogenetics.: Suchard MA & Rambaut A (2009) Bioinformatics 25, 1370-1376.

Reduced effectiveness of selection caused by a lack of recombination on the dot chromosome of Drosophila americana.: Betancourt AJ, Welch JJ & Charlesworth B (2009) Current Biology 19, 655-660.

Accommodating the effect of ancient DNA damage on inferences of demographic histories.: Rambaut A, Ho SYW, Drummond AJ & Shapiro B (2008) Mol Biol Evol 26, 245-248.

Divergence and polymorphism under the nearly neutral theory of molecular evolution.: Welch JJ, Eyre-Walker A & Waxman D (2008) J Mol Evol 67, 418-26.

Evolutionary genomics of host adaptation in vesicular stomatitis virus (VSV).: Remold SK, Rambaut A & Turner PE (2008) MBE 25, 1138-1147.

Correlates of substitution rate variation in mammalian protein-coding sequences.: Welch JJ, Bininda-Emonds ORP & Bromham L (2008) BMC Evol Biol 8, 53.

Complete list for: Molecular Evolution and Phylogenetic Analyses

Evolutionary Inference, Phylogenetic Methods, Population Genetic Models

Relaxed Phylogenetics and Dating with Confidence.: Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88.

Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences.: Shapiro B, Rambaut A & Drummond AJ (2006) Mol Biol Evol 23, 7-9.

Molecular dates for the "Cambrian explosion": the influence of prior assumptions.: Welch JJ, Fontanillas E & Bromham L (2005) Syst Biol 54, 672-678.

Molecular dating when rates vary.: Welch JJ & Bromham L (2005) Trends Ecol Evol 20, 320-327.

Bayesian coalescent inference of past population dynamics from molecular sequences.: Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185-1192.

Inference of viral evolutionary rates from molecular sequences.: Drummond A, Pybus OG & Rambaut A (2003) Adv Parasitology 54, 331-358.

Measurably evolving populations.: Drummond AJ, Pybus OG, Rambaut A, Forsberg R & Rodrigo AG (2003) Trends Ecol Evol 18, 481-488.

GENIE: estimating demographic history from molecular phylogenies.: Pybus OG & Rambaut A (2002) Bioinformatics 18, 1404-1405.

Inferring confidence sets of possibly misspecified gene trees.: Strimmer K & Rambaut A (2002) Proc Roy Soc B 269, 137-142.

An integrated framework for the inference of viral population history from reconstructed genealogies.: Pybus OG, Rambaut A & Harvey PH (2000) Genetics 155, 1429-1437.

Complete list for: Evolutionary Inference, Phylogenetic Methods, Population Genetic Models

The Comparative Method and Macro-Evolutionary Models

Testing the Island Rule: Primates as a case study.: Welch JJ (2009) Proc Roy Soc B 276, 675-682.

Calculating Independent Contrasts for the Comparative Study of Substitution Rates.: Welch JJ & Waxman D (2008) J Theor Biol 251, 667-678.

New inferences from tree shape: numbers of missing taxa and population growth rates.: Pybus OG, Rambaut A, Holmes EC & Harvey PH (2002) Syst Biol 51, 881-888.

Comparative analyses for adaptive radiations.: Harvey PH & Rambaut A (2000) Phil Trans Roy Soc B 355, 1599-1605.

Phylogenetic extinction rates and comparative methodology.: Harvey PH & Rambaut A (1998) Proc Roy Soc B 265, 1691-1696.

Bi-De: an application for simulating phylogenetic processes.: Rambaut A, Grassly NC, Nee S & Harvey PH (1996) Comput Appl Biosci 12, 469-471.

Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data.: Purvis A & Rambaut A (1995) Comput Appl Biosci 11, 247-251.

Complete list for: The Comparative Method and Macro-Evolutionary Models

General Evolutionary Biology and Ecology

The "island rule" and deep-sea gastropods: Re-examining the evidence.: Welch JJ (2010) PLoS One 5, e8776.

Breeding racehorses: what price good genes?.: Wilson AJ & Rambaut A (2008) Biology Letters 4, 173-175.

Fisher's Microscope and Haldane's Ellipse.: Waxman D & Welch JJ (2005) Am Nat 166, 447-457.

The nk Model and Population Genetics.: Welch JJ & Waxman D (2005) J Theor Biol 234, 329-340.

Accumulating Dobzhansky-Muller incompatibilities: reconciling theory with data.: Welch JJ (2004) Evolution 58, 1145-1156.

Adaptation and Species Range.: Peck JR & Welch JJ (2004) Evolution 58, 211-221.

Modularity and the Cost of Complexity.: Welch JJ & Waxman D (2003) Evolution 57, 1723-1734.

Non-equivalent loci and mutation-selection balance.: Waxman D & Welch JJ (2003) Theor Pop Biol 63, 339-345.

Non-equivalent loci and the distribution of mutant effects.: Welch JJ & Waxman D (2002) Genetics 161, 897-904.

Complete list for: General Evolutionary Biology and Ecology