Belshaw, Robert, De Oliveira, Tulio, Markowitz, Sidney, Rambaut, Andrew
The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide...
Many-core algorithms for statistical phylogenetics (2009)
Suchard, Marc A., Rambaut, Andrew
Motivation: Statistical phylogenetics is computationally intensive, resulting in considerable attention meted on techniques for parallelization. Codon-based models allow for independent rates of...
316 316 316 Increasing and Unusual Genetic Diversity of HIV-1 in the UK (2008)
Robert Gifford, Tulio De Oliveira, Andrew Rambaut, Richard E. Myers, Catherine V. Gale, David Dunn, ...
Phylogenetic analysis of human immunodeficiency type 1 (HIV-1) isolates from around the world reveals three major groups, M, O and N, each of which is proposed to have arisen independently via...
Episodic Sexual Transmission of HIV Revealed by Molecular Phylodynamics (2008)
Fraser Lewis, Gareth J. Hughes, Andrew Rambaut, Anton Pozniak
BackgroundThe structure of sexual contact networks plays a key role in the epidemiology of sexually transmitted infections, and their reconstruction from interview data has provided valuable insights...
Camacho, Ricardo, Rambaut, Andrew, ...
MOTIVATION: HIV-1 antiviral resistance is a major cause of antiviral treatment failure. The in vivo fitness landscape experienced by the virus in presence of treatment could in principle be used to...
Evolutionary Genomics of Host Adaptation in Vesicular Stomatitis Virus (2008)
Remold, Susanna K., Rambaut, Andrew, Turner, Paul E.
Populations experiencing similar selection pressures can sometimes diverge in the genetic architectures underlying evolved complex traits. We used RNA virus populations of large size and high...
De Oliveira, Tulio, Rambaut, Andrew, Pybus, Oliver G, Dunn, David, ...
With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this...
BEAST: Bayesian evolutionary analysis by sampling trees (2007)
Drummond, Alexei J, Rambaut, Andrew
Abstract Background The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference,...
The evolution of genome compression and genomic novelty in RNA viruses (2007)
Belshaw, Robert, Pybus, Oliver G., Rambaut, Andrew
The genomes of RNA viruses are characterized by their extremely small size and extremely high mutation rates (typically 10 kb and 10−4/base/replication cycle, respectively), traits that are thought...
Camacho, Ricardo, Shapiro, Beth, Rambaut, Andrew, ...
The human immunodeficiency virus (HIV) has a genome that is rich in adenine, and its rapid evolution shows an observed bias of guanine (G) to adenine (A) mutations. Two mechanisms have been proposed...
Vidal, Nicole, De Oliveira, Túlio, Peeters, Martine, Camacho, Ricardo, ...
HIV-1 is classified in 9 subtypes (A-D, F, G, H, J and K), sub-subtypes and several Circulating Recombinant Forms (CRFs). Due to the high level of genetic diversity within HIV-1 and to its worldwide...
Bayesian Estimation of Sequence Damage in Ancient DNA (2007)
Ho, Simon Y. W., Heupink, Tim H., Rambaut, Andrew, Shapiro, Beth
Bayesian Estimation of Sequence Damage in Ancient DNA (2007)
Ho, Simon Y. W., Heupink, Tim H., Rambaut, Andrew, Shapiro, Beth
DNA extracted from archaeological and paleontological remains is usually damaged by biochemical processes postmortem. Some of these processes lead to changes in the structure of the DNA molecule,...
Philippe Lemey, Alexei J. Drummond, Oliver G. Pybus, Beth Shapiro, Helena Barroso, ...
Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood...
Kosakovsky Pond, Sergei L, Drummond, Alexei J, Pybus, Oliver G, Shapiro, Beth, Barroso, Helena, ...
Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood...
Philippe Lemey, Alexei J. Drummond, Oliver G. Pybus, Beth Shapiro, Helena Barroso, ...
Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood...
BEAST: Bayesian evolutionary analysis by sampling trees (2007)
Drummond, Alexei James, Rambaut, Andrew
An open access copy of this article is available and complies with the copyright holder/publisher conditions.
Alexei J Drummond, Andrew Rambaut, Alexei J. Drummond, Andrew Rambaut, Alexei J. Drummond, Andrew Rambaut
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Pybus, Oliver G., Rambaut, Andrew, Belshaw, Robert, Freckleton, Robert P., Drummond, Alexei J., Holmes, Edward C.
Populations of RNA viruses are often characterized by abundant genetic variation. However, the relative fitness of these mutations is largely unknown, although this information is central to our...
Pybus, Oliver G., Rambaut, Andrew, Belshaw, Robert, Freckleton, Robert P., Drummond, Alexei J., Holmes, Edward C.
Populations of RNA viruses are often characterized by abundant genetic variation. However, the relative fitness of these mutations is largely unknown, although this information is central to our...
HIV evolutionary dynamics within and among hosts (2006)
Rambaut, Andrew, Pybus, Oliver G
The HIV evolutionary processes continuously unfold, leaving a measurable footprint in viral gene sequences. A variety of statistical models and inference techniques have been developed to reconstruct...
De Oliveira, Tulio, Rambaut, Andrew, Myers, Richard E, Gale, Catherine V, Dunn, David, ...
BACKGROUND: The routine use of drug resistance testing provides an abundant source of HIV-1 sequence data. However, it is not clear how reliable standard genotyping of these sequences is for...
Relaxed Phylogenetics and Dating with Confidence (2006)
Alexei J. Drummond, Matthew J. Phillips, Andrew Rambaut
This new method can simultaneously infer phylogeny and estimate the molecular clock. The authors run their method on several large alignments to show its phylogenetic accuracy and ability to infer a...
Relaxed Phylogenetics and Dating with Confidence (2006)
Alexei J. Drummond, Matthew J. Phillips, Andrew Rambaut
In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are...
Chung-chau Hon, Tsan-yuk Lam, Alexei Drummond, Andrew Rambaut, Yiu-fai Lee, Chi-wai Yip, ...
Infectious bursal disease virus (IBDV) is a birnavirus causing immunosuppressive disease in chickens. Emergence of the very virulent form of IBDV (vvIBDV) in the late 1980s dramatically changed the...
Shapiro, Beth, Rambaut, Andrew, Pybus, Oliver G., Holmes, Edward C.
RNA virus genomes are compact, often containing multiple overlapping reading frames and functional secondary structure. Consequently, it is thought that evolutionary interactions between nucleotide...
Shapiro, Beth, Rambaut, Andrew, Pybus, Oliver G., Holmes, Edward C.
RNA virus genomes are compact, often containing multiple overlapping reading frames and functional secondary structure. Consequently, it is thought that evolutionary interactions between nucleotide...
Heterotachy and Tree Building: A Case Study with Plastids and Eubacteria (2006)
Lockhart, Peter, Novis, Phil, Milligan, Brook G., Riden, Jamie, Rambaut, Andrew, Larkum, Tony
The nature of heterotachy at the center of recent controversy over the relative performance of tree-building methods is different from the form of heterotachy that has been inferred in empirical...
Shapiro, Beth, Rambaut, Andrew, Drummond, Alexei J.
Although phylogenetic inference of protein-coding sequences continues to dominate the literature, few analyses incorporate evolutionary models that consider the genetic code. This problem is...
Derdelinckx, Inge, Rambaut, Andrew, Dumont, Stephanie, Vermeulen, Steve, ...
Known human immunodeficiency virus (HIV) transmission histories are invaluable models for investigating the evolutionary and transmission dynamics of the virus and to assess the accuracy of...
Inge Derdelinckx, Andrew Rambaut, Kristel Van Laethem, Stephanie Dumont, Steve Vermeulen, Eric Van Wijngaerden
Known human immunodeficiency virus (HIV) transmission histories are invaluable models for investigating the evolutionary and transmission dynamics of the virus and to assess the accuracy of...
Heterotachy and Tree Building: A Case Study with Plastids and Eubacteria (2005)
Lockhart, Peter, Novis, Phil, Milligan, Brook G., Riden, Jamie, Rambaut, Andrew, Larkum, Tony
The nature of heterotachy at the centre of recent controversy over the relative performance of tree building methods is different from the form of heterotachy that has been inferred in empirical...
Shapiro, Beth, Rambaut, Andrew, Drummond, Alexei J.
Although phylogenetic inference of protein coding sequences continues to dominate the literature, few analyses incorporate evolutionary models that consider the genetic code. This problem is...
Heterotachy and Tree Building: A Case Study with Plastids and Eubacteria (2005)
Lockhart, Peter, Novis, Phil, Milligan, Brook G., Riden, Jamie, Rambaut, Andrew, Larkum, Tony
The nature of heterotachy at the centre of recent controversy over the relative performance of tree building methods is different from the form of heterotachy that has been inferred in empirical...
Shapiro, Beth, Rambaut, Andrew, Drummond, Alexei J.
Although phylogenetic inference of protein coding sequences continues to dominate the literature, few analyses incorporate evolutionary models that consider the genetic code. This problem is...
Magiorkinis, Emmanouil, Magiorkinis, Gkikas, Kiosses, Vassilios G, ...
The CRF04_cpx strains of HIV-1 accounts for approximately 2-10% of the infected population in Greece, across different transmission risk groups. CRF04_cpx was the lineage documented in an HIV-1...
The molecular population genetics of HIV-1 group O (2004)
Pybus, Oliver G, Rambaut, Andrew, Drummond, Alexei J, Robertson, David L, Roques, Pierre, ...
HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics...
Inferring the Rate and Time-Scale of Dengue Virus Evolution (2003)
Twiddy, S. Susanna, Holmes, Edward C., Rambaut, Andrew
Dengue is often referred to as an emerging disease because of the rapid increases in incidence and prevalence that have been observed in recent decades. To understand the rate at which genetic...
Lindell Bromham, Megan Woolfit, Andrew Rambaut
Molecular evolution has been considered to be essentially a stochastic process, little influenced by the pace of phenotypic change. This assumption was challenged by a study that demonstrated an...
Motivation: TipDate is a program that will use sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate...
Motivation: TipDate is a program that will use sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate...
Motivation: TipDate is a program that will use sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate...
Motivation: TipDate is a program that will use sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate...
Motivation: TipDate is a program that will use sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate...
Genetic analysis of West Nile New York 1999 encephalitis virus (1999)
Jia, Xi-Yu, Briese, Thomas, Jordan, Ingo, Rambaut, Andrew, Chi, Han Chang, Mackenzie, John S., ...
Analysis of the genome of the flavivirus responsible for the 1999 New York City encephalitis epidemic cloned from human brain by reverse-transcription polymerase chain reaction indicates its identity...
Genetic analysis of West Nile New York 1999 encephalitis virus (1999)
Jia, Xi-Yu, Briese, Thomas, Jordan, Ingo, Rambaut, Andrew, Chi, Han Chang, Mackenzie, John S., ...
Analysis of the genome of the flavivirus responsible for the 1999 New York City encephalitis epidemic cloned from human brain by reverse-transcription polymerase chain reaction indicates its identity...
The inference of evolutionary and population dynamic processes from molecular phylogenies / (1997)
Includes bibliographical references.
Rambaut, Andrew, Grass, Nicholas C.
Motivation: Seq-Gen is a program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution...
Rambaut, Andrew, Harvey, Paul H., Nee, Sean
Motivation. Phylogenetic trees constructed from molecular sequences contain information about the evolutionary or population dynamical processes that created them. Here we describe a computer package...
Bi-De: an application for simulating phylogenetic processes (1996)
Rambaut, Andrew, Grassly, Nicholas C., Nee, Sean, Harvey, Paul H.
Birth-Death (Bi-De) is an application for the Apple Macintosh which simulates the growth of phylogenetic trees using various models of lineage birth and death. The trees produced are intended to be...
CAIC is an application for the Apple Macintosh which allows the valid analysis of comparative (multi-species) data sets that include continuous variables. Comparison among species is the most common...
Widespread intra-serotype recombination in natural populations of dengue virus
Worobey, Michael, Rambaut, Andrew, Holmes, Edward C.
Diversity analysis of 71 published dengue virus gene sequences revealed several strains that appeared to be mosaics comprising gene regions with conflicting evolutionary histories. Subsequent maximum...
Testing the Cambrian explosion hypothesis by using a molecular dating technique
Bromham, Lindell, Rambaut, Andrew, Fortey, Richard, Cooper, Alan, Penny, David
Molecular studies have the potential to shed light on the origin of the animal phyla by providing independent estimates of the divergence times, but have been criticized for failing to account...
Molecular Footprint of Drug-Selective Pressure in a Human Immunodeficiency Virus Transmission Chain†
Lemey, Philippe, Derdelinckx, Inge, Rambaut, Andrew, Van Laethem, Kristel, Dumont, Stephanie, Vermeulen, Steve, ...
Known human immunodeficiency virus (HIV) transmission histories are invaluable models for investigating the evolutionary and transmission dynamics of the virus and to assess the accuracy of...
Relaxed Phylogenetics and Dating with Confidence
Drummond, Alexei J, Ho, Simon Y. W, Phillips, Matthew J, Rambaut, Andrew
In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are...
The molecular population genetics of HIV-1 group O.
Lemey, Philippe, Pybus, Oliver G, Rambaut, Andrew, Drummond, Alexei J, Robertson, David L, Roques, Pierre, ...
HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics...
Widespread intra-serotype recombination in natural populations of dengue virus
Worobey, Michael, Rambaut, Andrew, Holmes, Edward C.
Diversity analysis of 71 published dengue virus gene sequences revealed several strains that appeared to be mosaics comprising gene regions with conflicting evolutionary histories. Subsequent maximum...
Testing the Cambrian explosion hypothesis by using a molecular dating technique
Bromham, Lindell, Rambaut, Andrew, Fortey, Richard, Cooper, Alan, Penny, David
Molecular studies have the potential to shed light on the origin of the animal phyla by providing independent estimates of the divergence times, but have been criticized for failing to account...
Molecular Footprint of Drug-Selective Pressure in a Human Immunodeficiency Virus Transmission Chain†
Lemey, Philippe, Derdelinckx, Inge, Rambaut, Andrew, Van Laethem, Kristel, Dumont, Stephanie, Vermeulen, Steve, ...
Known human immunodeficiency virus (HIV) transmission histories are invaluable models for investigating the evolutionary and transmission dynamics of the virus and to assess the accuracy of...
Relaxed Phylogenetics and Dating with Confidence
Drummond, Alexei J, Ho, Simon Y. W, Phillips, Matthew J, Rambaut, Andrew
In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are...
The molecular population genetics of HIV-1 group O.
Lemey, Philippe, Pybus, Oliver G, Rambaut, Andrew, Drummond, Alexei J, Robertson, David L, Roques, Pierre, ...
HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics...
Hon, Chung-Chau, Lam, Tsan-Yuk, Drummond, Alexei, Rambaut, Andrew, Lee, Yiu-Fai, Yip, Chi-Wai, ...
Infectious bursal disease virus (IBDV) is a birnavirus causing immunosuppressive disease in chickens. Emergence of the very virulent form of IBDV (vvIBDV) in the late 1980s dramatically changed the...
JC Virus Evolution and Its Association with Human Populations†
Shackelton, Laura A., Rambaut, Andrew, Pybus, Oliver G., Holmes, Edward C.
The ubiquitous human polyomavirus JC (JCV) is a small double-stranded DNA virus that establishes a persistent infection, and it is often transmitted from parents to children. There are at least 14...
Lemey, Philippe, Kosakovsky Pond, Sergei L, Drummond, Alexei J, Pybus, Oliver G, Shapiro, Beth, Barroso, Helena, ...
Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood...
Inferring confidence sets of possibly misspecified gene trees.
Strimmer, Korbinian, Rambaut, Andrew
The problem of inferring confidence sets of gene trees is discussed without assuming that the substitution model or the branching pattern of any of the investigated trees is correct. In this case,...
Viral evolution and the emergence of SARS coronavirus.
Holmes, Edward C, Rambaut, Andrew
The recent appearance of severe acute respiratory syndrome coronavirus (SARS-CoV) highlights the continual threat to human health posed by emerging viruses. However, the central processes in the...
Pillay, Deenan, Rambaut, Andrew, Geretti, Anna Maria, Brown, Andrew J Leigh
Criminal convictions relying solely on this to establish transmission are unsafe
Abecasis, Ana B., Lemey, Philippe, Vidal, Nicole, De Oliveira, Túlio, Peeters, Martine, Camacho, Ricardo, ...
Human immunodeficiency virus type 1 (HIV-1) is classified in nine subtypes (A to D, F, G, H, J, and K), a number of subsubtypes, and several circulating recombinant forms (CRFs). Due to the high...
Episodic Sexual Transmission of HIV Revealed by Molecular Phylodynamics
Lewis, Fraser, Hughes, Gareth J, Rambaut, Andrew, Pozniak, Anton, Leigh Brown, Andrew J.
Using viral genotype data from HIV drug resistance testing at a London clinic, Andrew Leigh Brown and colleagues derive the structure of the transmission network through phylogenetic analysis.
The evolution of genome compression and genomic novelty in RNA viruses
Belshaw, Robert, Pybus, Oliver G., Rambaut, Andrew
The genomes of RNA viruses are characterized by their extremely small size and extremely high mutation rates (typically 10 kb and 10−4/base/replication cycle, respectively), traits that are thought...
Gifford, Robert J., De Oliveira, Tulio, Rambaut, Andrew, Pybus, Oliver G., Dunn, David, Vandamme, Anne-Mieke, ...
With ongoing generation of viral genetic diversity and increasing levels of migration, the global human immunodeficiency virus type 1 (HIV-1) epidemic is becoming increasingly heterogeneous. In this...
The emergence of HIV/AIDS in the Americas and beyond
Gilbert, M. Thomas P., Rambaut, Andrew, Wlasiuk, Gabriela, Spira, Thomas J., Pitchenik, Arthur E., Worobey, Michael
HIV-1 group M subtype B was the first HIV discovered and is the predominant variant of AIDS virus in most countries outside of sub-Saharan Africa. However, the circumstances of its origin and...
Reply to Pape et al.: The phylogeography of HIV-1 group M subtype B
Worobey, Michael, Pitchenik, Arthur E., Gilbert, M. Thomas P., Wlasiuk, Gabriela, Rambaut, Andrew
Armitage, Andrew E., Katzourakis, Aris, De Oliveira, Tulio, Welch, John J., Belshaw, Robert, Bishop, Kate N., ...
The human polynucleotide cytidine deaminases APOBEC3G (hA3G) and APOBEC3F (hA3F) are antiviral restriction factors capable of inducing extensive plus-strand guanine-to-adenine (G-to-A) hypermutation...
Breeding racehorses: what price good genes?
Wilson, Alastair J, Rambaut, Andrew
Horse racing is a multi-million pound industry, in which genetic information is increasingly used to optimize breeding programmes. To maximize the probability of producing a successful offspring, the...
Belshaw, Robert, De Oliveira, Tulio, Markowitz, Sidney, Rambaut, Andrew
The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide...
Phylogenetic Analysis of a Human Isolate from the 2000 Israel West Nile virus Epidemic
Briese, Thomas, Rambaut, Andrew, Pathmajeyan, Melissa, Bishara, Jihad, Weinberger, Miriam, Pitlik, Silvio, ...
Specimens from a patient of the 2000 Israel West Nile virus epidemic were analyzed by reverse transcription-polymerase chain reaction. Products corresponding to E, NS3, and NS5 sequences were...
Bayesian Phylogeography Finds Its Roots
Lemey, Philippe, Rambaut, Andrew, Drummond, Alexei J., Suchard, Marc A.
As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. Unfortunately, inference of...
Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom
Hughes, Gareth J., Fearnhill, Esther, Dunn, David, Lycett, Samantha J., Rambaut, Andrew, Leigh Brown, Andrew J.
The heterosexual risk group has become the largest HIV infected group in the United Kingdom during the last 10 years, but little is known of the network structure and dynamics of viral transmission...
The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic
Rambaut, Andrew, Holmes, Edward
Swine-origin pandemic human influenza A virus (H1N1pdm) has spread rapidly around the world since its initial documentation in April 2009. Here we have updated initial estimates of the rate of...
Lemey, Philippe, Suchard, Marc, Rambaut, Andrew
Here, we present an analysis of the H1N1pdm genetic data sampled over the initial stages in the epidemic. To infer phylodynamic spread in time and space we employ a recently developed Bayesian...