Andrew Rambaut | Academic Influence

Q: What Schools Are Affiliated With Andrew Rambaut

Andrew Rambaut is affiliated with the following schools: University of Oxford, Douglas College, University of Edinburgh, University of Alaska Fairbanks

Why Is Andrew Rambaut Influential?

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According to Wikipedia, Andrew Rambaut is a British evolutionary biologist, professor of molecular evolution at the University of Edinburgh. Education Rambaut earned a Bachelor of Science degree in Zoology from the University of Edinburgh in 1993 followed by a DPhil in Zoology from the University of Oxford in 1997 supervised by Paul H. Harvey.

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Andrew Rambaut's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

BEAST: Bayesian evolutionary analysis by sampling trees (2007) (11768)
Bayesian Phylogenetics with BEAUti and the BEAST 1.7 (2012) (8908)
Relaxed Phylogenetics and Dating with Confidence (2006) (5634)
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 (2018) (4973)
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis (2014) (4854)
The proximal origin of SARS-CoV-2 (2020) (3890)
Bayesian coalescent inference of past population dynamics from molecular sequences. (2005) (2792)
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic (2009) (2067)
Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings (2009) (1932)
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 (2018) (1923)
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology (2020) (1898)
SARS-CoV-2 variants, spike mutations and immune escape (2021) (1886)
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis (2018) (1760)
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees (1997) (1610)
Bayesian Phylogeography Finds Its Roots (2009) (1452)
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) (2016) (1331)
Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data (1995) (1170)
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak (2014) (1126)
Real-time, portable genome sequencing for Ebola surveillance (2016) (1065)
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. (2012) (951)
Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil (2021) (942)
The genomic and epidemiological dynamics of human influenza A virus (2008) (897)
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa (2021) (860)
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity (2020) (819)
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (2021) (806)
Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (2021) (806)
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic (2020) (713)
Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. (2006) (695)
SARS-CoV-2 evolution during treatment of chronic infection (2021) (647)
Rise and Fall of the Beringian Steppe Bison (2004) (647)
Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis (2002) (635)
The early spread and epidemic ignition of HIV-1 in human populations (2014) (585)
The causes and consequences of HIV evolution (2004) (583)
Phylogeography takes a relaxed random walk in continuous space and time. (2010) (565)
Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data (2021) (557)
Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool (2021) (537)
Evolutionary analysis of the dynamics of viral infectious disease (2009) (530)
Persistent HIV-1 replication maintains the tissue reservoir during therapy (2015) (530)
BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics (2011) (522)
Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study (2021) (488)
Evolution and epidemic spread of SARS-CoV-2 in Brazil (2020) (459)
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics (2011) (458)
Mapping the human genetic architecture of COVID-19 (2021) (455)
Inferring confidence sets of possibly misspecified gene trees (2002) (453)
Establishment and cryptic transmission of Zika virus in Brazil and the Americas (2017) (450)
The Epidemic Behavior of the Hepatitis C Virus (2001) (449)
Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity (2021) (443)
Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution (2001) (435)
The genesis and source of the H7N9 influenza viruses causing human infections in China (2013) (430)
Genomic characterisation of an emergent SARS- CoV-2 lineage in Manaus: preliminary findings (2021) (419)
Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. (2008) (407)
Global circulation patterns of seasonal influenza viruses vary with antigenic drift (2015) (402)
Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. (2013) (402)
Clinical features and virological analysis of a case of Middle East respiratory syndrome coronavirus infection (2013) (395)
Many-core algorithms for statistical phylogenetics (2009) (390)
Phylogenetic evidence for recombination in dengue virus. (1999) (384)
Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus (2009) (384)
An integrated framework for the inference of viral population history from reconstructed genealogies. (2000) (379)
Episodic Sexual Transmission of HIV Revealed by Molecular Phylodynamics (2008) (376)
Measurably evolving populations (2003) (370)
Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies (2000) (360)
Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility (2013) (341)
The emergence of HIV/AIDS in the Americas and beyond (2007) (325)
SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes. (2016) (325)
Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study (2013) (324)
Virus genomes reveal factors that spread and sustained the Ebola epidemic (2017) (319)
Zika virus evolution and spread in the Americas (2017) (313)
Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2 (2014) (289)
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK (2020) (288)
Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7 (2021) (285)
Estimating divergence dates from molecular sequences. (1998) (281)
Temporal signal and the phylodynamic threshold of SARS-CoV-2 (2020) (278)
The emergence of SARS-CoV-2 in Europe and North America (2020) (277)
Temporal and spatial analysis of the 2014–2015 Ebola virus outbreak in West Africa (2015) (277)
Integrating influenza antigenic dynamics with molecular evolution (2013) (275)
Genomic epidemiology reveals multiple introductions of Zika virus into the United States (2017) (272)
Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus (2014) (265)
Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone (2015) (262)
The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. (2003) (260)
Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China (2020) (259)
Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands (2020) (255)
Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline (2011) (252)
Tracking virus outbreaks in the twenty-first century (2018) (246)
Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses (2010) (245)
HIV evolutionary dynamics within and among hosts. (2006) (241)
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa (2022) (237)
The origins of SARS-CoV-2: A critical review (2021) (235)
The evolution of Ebola virus: Insights from the 2013–2016 epidemic (2016) (232)
Inferring the rate and time-scale of dengue virus evolution. (2003) (229)
Widespread intra-serotype recombination in natural populations of dengue virus. (1999) (228)
A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology (2020) (227)
Unifying the spatial epidemiology and molecular evolution of emerging epidemics (2012) (217)
Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny (2012) (215)
Genesis and pathogenesis of the 1918 pandemic H1N1 influenza A virus (2014) (206)
Determinants of rate variation in mammalian DNA sequence evolution (1996) (202)
A synchronized global sweep of the internal genes of modern avian influenza virus (2014) (200)
Origins of the 2009 H1N1 influenza pandemic in swine in Mexico (2016) (199)
Livestock Origin for a Human Pandemic Clone of Community-Associated Methicillin-Resistant Staphylococcus aureus (2013) (189)
Evolutionary Genomics of Staphylococcus aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation (2010) (189)
Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days (2016) (186)
COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study (2020) (182)
Inference of viral evolutionary rates from molecular sequences. (2003) (181)
Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom (2009) (180)
Genetic analysis of West Nile New York 1999 encephalitis virus (1999) (177)
Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus (2012) (176)
Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013–2016 Epidemic (2016) (175)
Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics (2007) (174)
MERS-CoV spillover at the camel-human interface (2017) (173)
Flight of the dodo. (2002) (170)
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse (2021) (168)
Human immunodeficiency virus: Phylogeny and the origin of HIV-1 (2001) (167)
Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus (2013) (165)
Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 (2020) (163)
Viral evolution and the emergence of SARS coronavirus. (2004) (162)
Inferring population history from molecular phylogenies. (1995) (161)
Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans (2011) (157)
Phylodynamic Reconstruction Reveals Norovirus GII.4 Epidemic Expansions and their Molecular Determinants (2010) (152)
Testing the Cambrian explosion hypothesis by using a molecular dating technique. (1998) (151)
Pacing a small cage: mutation and RNA viruses (2008) (150)
The evolution of genome compression and genomic novelty in RNA viruses. (2007) (149)
Comparative analyses for adaptive radiations. (2000) (145)
MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity (2018) (145)
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. (2021) (145)
Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus (2010) (141)
Phylogenetic evidence for deleterious mutation load in RNA viruses and its contribution to viral evolution. (2007) (139)
The Molecular Population Genetics of HIV-1 Group O (2004) (138)
Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study (2021) (136)
Molecular Epidemiology: HIV-1 and HCV sequences from Libyan outbreak (2006) (135)
The Power of Relative Rates Tests Depends on the Data (2000) (133)
GENIE: estimating demographic history from molecular phylogenies (2002) (130)
TESTING THE RELATIONSHIP BETWEEN MORPHOLOGICAL AND MOLECULAR RATES OF CHANGE ALONG PHYLOGENIES (2002) (130)
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway (2022) (130)
Spatial Dynamics of Human-Origin H1 Influenza A Virus in North American Swine (2011) (128)
Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints (2013) (124)
A Bayesian phylogenetic method to estimate unknown sequence ages. (2011) (123)
Phylogeography and population dynamics of dengue viruses in the Americas. (2012) (121)
Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2 (2020) (116)
Real-time digital pathogen surveillance — the time is now (2015) (113)
Global migration of influenza A viruses in swine (2015) (111)
BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics (2019) (111)
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus (2022) (111)
Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis (2011) (110)
The effect of genetic structure on molecular dating and tests for temporal signal (2015) (110)
Pandemics: spend on surveillance, not prediction (2018) (109)
Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic (2021) (108)
Origin of AIDS: Contaminated polio vaccine theory refuted (2004) (106)
Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases (2016) (103)
The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity (2020) (103)
Recombination Confounds the Early Evolutionary History of Human Immunodeficiency Virus Type 1: Subtype G Is a Circulating Recombinant Form (2007) (100)
Revealing the history of infectious disease epidemics through phylogenetic trees. (1995) (99)
Phylogenetic Analysis Reveals a Correlation between the Expansion of Very Virulent Infectious Bursal Disease Virus and Reassortment of Its Genome Segment B (2006) (98)
Development and validation of the ISARIC 4C Deterioration model for adults hospitalised with COVID-19: a prospective cohort study (2021) (98)
Endemic Dengue Associated with the Co-Circulation of Multiple Viral Lineages and Localized Density-Dependent Transmission (2011) (97)
Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence (2021) (96)
Heterotachy and tree building: a case study with plastids and eubacteria. (2006) (96)
JC Virus Evolution and Its Association with Human Populations (2006) (96)
Evolution and Spread of Ebola Virus in Liberia, 2014-2015. (2015) (95)
Risk of adverse outcomes in patients with underlying respiratory conditions admitted to hospital with COVID-19: a national, multicentre prospective cohort study using the ISARIC WHO Clinical Characterisation Protocol UK (2021) (94)
Phylogenetic Surveillance of Viral Genetic Diversity and the Evolving Molecular Epidemiology of Human Immunodeficiency Virus Type 1 (2007) (94)
Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2 (2020) (94)
The evolutionary dynamics of endogenous retroviruses. (2005) (94)
Canalization of the evolutionary trajectory of the human influenza virus (2011) (93)
Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak (2014) (92)
Recombination between sequences of hepatitis B virus from different genotypes (1996) (91)
The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic (2022) (89)
The early molecular epidemiology of the swine-origin A/H1N1 human influenza pandemic (2009) (88)
Conserved Footprints of APOBEC3G on Hypermutated Human Immunodeficiency Virus Type 1 and Human Endogenous Retrovirus HERV-K(HML2) Sequences (2008) (86)
Emerging Concepts of Data Integration in Pathogen Phylodynamics (2016) (86)
Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication (2012) (85)
New inferences from tree shape: numbers of missing taxa and population growth rates. (2002) (85)
The Phylogenetic Handbook: Bayesian evolutionary analysis by sampling trees (2009) (84)
Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set (2014) (83)
Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth. (2005) (83)
The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach (2010) (83)
HIV Sequence Compendium 2010 (2010) (82)
Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant (2021) (82)
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland (2020) (82)
Toward a quantitative understanding of viral phylogeography. (2011) (81)
Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management (2015) (81)
The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates (2014) (81)
Evolutionary genomics of host adaptation in vesicular stomatitis virus. (2008) (81)
Reconstructing the initial global spread of a human influenza pandemic: A Bayesian spatial-temporal model for the global spread of H1N1pdm. (2009) (80)
Importation and early local transmission of COVID-19 in Brazil, 2020 (2020) (78)
Characterisation of in-hospital complications associated with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, multicentre cohort study (2021) (77)
Molecular Footprint of Drug-Selective Pressure in a Human Immunodeficiency Virus Transmission Chain (2005) (77)
HIV Sequence Compendium 2018 (2018) (74)
Inferring Heterogeneous Evolutionary Processes Through Time: from Sequence Substitution to Phylogeography (2013) (71)
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II (2012) (71)
Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus. (2002) (68)
Genome-wide evolutionary dynamics of influenza B viruses on a global scale (2017) (67)
Evolutionary rate differences in trypanosomes. (2001) (67)
The emergence of SARS-CoV-2 in Europe and the US (2020) (65)
APOBEC3G-Induced Hypermutation of Human Immunodeficiency Virus Type-1 Is Typically a Discrete “All or Nothing” Phenomenon (2012) (65)
Reassortment between Influenza B Lineages and the Emergence of a Coadapted PB1–PB2–HA Gene Complex (2014) (65)
Accommodating the effect of ancient DNA damage on inferences of demographic histories. (2009) (64)
MERS-CoV recombination: implications about the reservoir and potential for adaptation (2015) (63)
Phylogenetic extinction rates and comparative methodology (1998) (63)
No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al.). (2006) (62)
Human Origins and Ancient Human DNA (2001) (62)
Reduced evolutionary rate in reemerged Ebola virus transmission chains (2016) (61)
Detection of neutralising antibodies to SARS-CoV-2 to determine population exposure in Scottish blood donors between March and May 2020 (2020) (60)
Genomic reconstruction of the SARS-CoV-2 epidemic in England (2021) (59)
Reconstructing the initial global spread of a human influenza pandemic (2009) (58)
Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting (2016) (57)
Changes in in-hospital mortality in the first wave of COVID-19: a multicentre prospective observational cohort study using the WHO Clinical Characterisation Protocol UK (2021) (56)
Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks (2021) (56)
Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak (2017) (56)
Origin and Evolution of the Unique Hepatitis C Virus Circulating Recombinant Form 2k/1b (2011) (55)
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2 (2022) (55)
The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study (2016) (54)
Reconstructing Geographical Movements and Host Species Transitions of Foot-and-Mouth Disease Virus Serotype SAT 2 (2013) (54)
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch (2021) (53)
Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation (2011) (53)
Bayesian estimation of sequence damage in ancient DNA. (2007) (53)
The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases (2015) (52)
End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences (1997) (52)
The evolutionary dynamics of canid and mongoose rabies virus in southern Africa (2007) (51)
A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution. (2006) (49)
Relaxed phylogenetics and the palaeoptera problem: resolving deep ancestral splits in the insect phylogeny. (2013) (49)
Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology (2021) (48)
Improving pandemic influenza risk assessment (2014) (47)
PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees (1997) (47)
Explorer BEAST : Bayesian evolutionary analysis by sampling trees (2017) (46)
Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda (2021) (45)
A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic (2021) (45)
Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment (2008) (43)
Non-steroidal anti-inflammatory drug use and outcomes of COVID-19 in the ISARIC Clinical Characterisation Protocol UK cohort: a matched, prospective cohort study (2021) (42)
OutbreakTools: A new platform for disease outbreak analysis using the R software (2014) (41)
Complete nucleotide sequence and transcriptional analysis of snakehead fish retrovirus (1996) (41)
Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda (2020) (41)
The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK (2022) (39)
Epidemiology: Sexual transmission of HIV in Africa (2003) (38)
Early Insights from Statistical and Mathematical Modeling of Key Epidemiologic Parameters of COVID-19 (2020) (38)
HIV Sequence Compendium 2015 (2015) (38)
Identification of common deletions in the spike protein of SARS-CoV-2. (2020) (38)
Phylogenetic Analysis of a Human Isolate from the 2000 Israel West Nile virus Epidemic (2002) (38)
CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance (2021) (37)
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST (2017) (37)
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) (37)
Evolutionary epidemiology: preparing for an age of genomic plenty (2013) (36)
Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity (2006) (36)
Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates (2019) (36)
BEAST2: Bayesian evolutionary analysis sampling trees (2014) (34)
HIV phylogenetics (2007) (34)
Real-time characterization of the molecular epidemiology of an influenza pandemic (2013) (32)
Estimating the Rate of Intersubtype Recombination in Early HIV-1 Group M Strains (2012) (32)
Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors (2018) (32)
Phylogenetic Reconstruction of a Known HIV-1 CRF04_cpx Transmission Network Using Maximum Likelihood and Bayesian Methods (2004) (30)
Multiple introductions of salmonid alphavirus from a wild reservoir have caused independent and self-sustainable epizootics in aquaculture. (2014) (29)
Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo (2007) (29)
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios (2013) (28)
Elucidating the Population Histories and Transmission Dynamics of Papillomaviruses Using Phylogenetic Trees (1997) (27)
Context-specific emergence and growth of the SARS-CoV-2 Delta variant (2021) (26)
Using genomics data to reconstruct transmission trees during disease outbreaks. (2016) (26)
Conserved Footprints of APOBEC 3 G on Hypermutated Human Immunodeficiency Virus Type 1 and Human Endogenous Retrovirus HERV-K ( HML 2 ) Sequences † (2008) (26)
Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences (2021) (25)
Bi-De: an application for simulating phylogenetic processes (1996) (25)
Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution (2015) (23)
Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence (2020) (23)
PANGEA-HIV 2: Phylogenetics And Networks for Generalised Epidemics in Africa (2019) (23)
Analysis of the medium (M) segment sequence of Guaroa virus and its comparison to other orthobunyaviruses. (2004) (23)
Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014–2015 (2016) (22)
Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America (2021) (21)
Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands (2020) (21)
An early warning system for emerging SARS-CoV-2 variants (2022) (19)
Online Bayesian Phylodynamic Inference in BEAST with Application to Epidemic Reconstruction (2020) (19)
Ebola Virus Transmission Initiated by Systemic Ebola Virus Disease Relapse (2021) (19)
The RNA Virus Database (2008) (19)
SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination (2018) (19)
Epidemic History and Iatrogenic Transmission of Blood-borne Viruses in Mid-20th Century Kinshasa. (2016) (18)
Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity (2021) (18)
Testing the Extent of Sequence Similarity Among Viroids, Satellite RNAs, and Hepatitis Delta Virus (2000) (18)
Massive Parallelization Boosts Big Bayesian Multidimensional Scaling (2019) (18)
Rapid and Sensitive Direct Detection and Identification of Poliovirus from Stool and Environmental Surveillance Samples by Use of Nanopore Sequencing (2020) (17)
Gradients do grow on trees: a linear-time 𝒪 (N)-dimensional gradient for statistical phylogenetics. (2020) (17)
Preferential detection of HIV subtype C' over subtype A in cervical cells from a dually infected woman. (2005) (17)
Identification of a common deletion in the spike protein of SARS-CoV-2 (2020) (17)
Origin and fate of A/H1N1 influenza in Scotland during 2009 (2012) (16)
Possible Footprints of APOBEC3F and/or Other APOBEC3 Deaminases, but Not APOBEC3G, on HIV-1 from Patients with Acute/Early and Chronic Infections (2014) (16)
Hepatitis B virus has a recent new world evolutionary origin (1998) (15)
Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway (2022) (15)
Monitoring key epidemiological parameters of SARS-CoV-2 transmission (2021) (15)
MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance (2020) (15)
Relax, Keep Walking — A Practical Guide to Continuous Phylogeographic Inference with BEAST (2021) (14)
Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer (2022) (14)
Breeding racehorses: what price good genes? (2008) (14)
Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England (2021) (14)
Modelling the impact of co-circulating low pathogenic avian influenza viruses on epidemics of highly pathogenic avian influenza in poultry. (2016) (13)
Author Correction: Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands (2020) (13)
COVID-19 in healthcare workers in three hospitals in the South of the Netherlands, March 2020 (2020) (13)
Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo (2019) (13)
Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2 (2021) (12)
Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic (2021) (12)
Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. (2020) (12)
Context-specific emergence and growth of the SARS-CoV-2 Delta variant (2022) (12)
Correction: MERS-CoV spillover at the camel-human interface (2018) (12)
Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022 (2022) (11)
The seasonal flight of influenza: a unified framework for spatiotemporal hypothesis testing (2012) (11)
Population Genetics of HIV: Parameter Estimation Using Genealogy-based Methods (2002) (11)
Reply to Pape et al.: The phylogeography of HIV-1 group M subtype B (2008) (11)
Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building (2018) (11)
Isolation and sequence analysis of a cDNA encoding the c subunit of a vacuolar-type H+-ATPase from the CAM plant Kalanchoë daigremontiana (1996) (10)
Implementation of corticosteroids in treatment of COVID-19 in the ISARIC WHO Clinical Characterisation Protocol UK: prospective, cohort study (2022) (10)
Longitudinal population analysis of dual infection with recombination in two strains of HIV type 1 subtype B in an individual from a Phase 3 HIV vaccine efficacy trial. (2006) (10)
Inferring the population history of an epidemic from a phylogenetic tree. (1996) (9)
Comment on “Mutation rate and genotype variation of Ebola virus from Mali case sequences” (2016) (9)
Genomic Sequencing of SARS-COV-2 in Rwanda: evolution and regional dynamics (2021) (9)
Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic (2016) (9)
Influenza: Making Privileged Data Public Response (2009) (8)
Relationship between haemagglutination inhibition titre and immunity to influenza in ferrets (2015) (8)
Genomics-informed outbreak investigations of SARS-CoV-2 using civet (2021) (8)
Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination (2021) (7)
Distinct clinical symptom patterns in patients hospitalised with COVID-19 in an analysis of 59,011 patients in the ISARIC-4C study (2022) (7)
Quantifying the contribution of different aged men and women to onwards transmission of HIV-1 in generalised epidemics in sub-Saharan Africa: A modelling and phylogenetics approach from the HPTN071 (PopART) trial (2019) (7)
Methylation-Based Age Estimation in a Wild Mouse (2020) (6)
Livestock origin for a human pandemic clone of community- associated MRSA (2013) (5)
Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission (2022) (5)
Spatio-temporal Dynamics of Foot-and-Mouth Disease Virus in South America (2015) (5)
Determinants of dengue virus dispersal in the Americas (2020) (5)
Viral evolution and the emergence of SARS (2004) (5)
High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE. (2019) (5)
Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza (2017) (5)
CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance (2021) (5)
Genome sequencing reveals Zika virus diversity and spread in the Americas (2017) (5)
Multiple introductions of Zika virus into the United States revealed through genomic epidemiology (2017) (5)
Lorenzo-Redondo et al. reply (2017) (5)
Circulating SARS-CoV-2 (2021) (4)
Putative APOBEC3 deaminase editing in MPXV as evidence for sustained human transmission since at least 2016 (2023) (4)
Explorer Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H 3 N 2 (2017) (4)
Molecular Tracing of the Emergence, Adaptation and Transmission of Hospital-Associated MRSA (2012) (4)
Edinburgh Research Explorer Revealing the sequence and resulting cellular morphology of receptor-ligand interactions during Plasmodium falciparum invasion of erythrocytes (2015) (4)
Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing (2020) (4)
New nomenclature for mpox (monkeypox) and monkeypox virus clades (2023) (3)
Explorer SPREAD : spatial phylogenetic reconstruction of evolutionary dynamics (2011) (3)
Correction: Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus (2011) (3)
Data from: Integrating influenza antigenic dynamics with molecular evolution (2014) (3)
Automated Agnostic Designation of Pathogen Lineages (2023) (2)
Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1 (2023) (2)
Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences (2022) (2)
Phylogenetic analysis reveals coincidence of the expansion of very virulent Infectious Bursal Disease Virus and the reassortment of its genome segment B (2006) (2)
Recent evolution patterns of Ebola virus inferred from patient samples collected from February-May 2015 with direct deep sequencing in Sierra Leone. (2015) (2)
Gradients do grow on trees: a linear-time ${\cal O}\hspace{-0.2em}\left( N \right)$-dimensional gradient for statistical phylogenetics (2019) (2)
Different Coexisting Mpox Lineages Were Continuously Circulating in Humans Prior to 2022 (2023) (1)
Context-specific emergence and growth of the SARS-CoV-2 Delta variant (2021) (1)
Using Molecular Data to Estimate Divergence Times (2007) (1)
The genomic epidemiology of SARS-CoV-2 variants of concern in Kenya (2022) (1)
Evolutionary Dynamics of Local Pandemic H1N1/09 Influenza Lineages Revealed 1 (2011) (1)
Establishment and early spread of the AIDS pandemic (2014) (1)
Author response: Improving pandemic influenza risk assessment (2014) (1)
Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning (2022) (1)
Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes (2023) (1)
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios (2014) (1)
Faria populations The early spread and epidemic ignition of HIV-1 in human (2014) (1)
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II (2012) (1)
Adaptive MCMC for multi-partite data in Bayesian Phylogenetics (2018) (1)
Canalization of the evolutionary trajectory of the human influenza virus (2012) (1)
SPREAD 4: online visualisation of pathogen phylogeographic reconstructions (2022) (1)
The proximal origin of SARS-CoV-2 (2020) (1)
Publisher Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland (2021) (1)
Form 2 k / 1 b Hepatitis C Virus Circulating Recombinant Origin and Evolution of the Unique (2012) (1)
A39 Reconstruction of Ebola chains of transmission using sequence and epidemiological data (2019) (0)
Understanding the adenine richness of the HIV genome through the estimation of misincorporation rates in viv (2007) (0)
Spatio-temporal Dynamics of Foot-and-Mouth Disease Virus in (2015) (0)
Software for Systematics and Evolution (2016) (0)
The emergence and early dissemination of pandemic Human Immunodeficiency virus type 1 (2012) (0)
Staphylococcus aureus Community-Associated Methicillin-Resistant Livestock Origin for a Human Pandemic Clone of 2013 (2013) (0)
Bayesian phylogeographic reconstruction of HIV-1 diffusion dynamics (2009) (0)
artic-network/fieldbioinformatics: 1.2.0 (2021) (0)
Quantitative deep sequencing and HIV-1 population dynamics (2010) (0)
Tracing virus migration using Bayesian phylogeographic inference (2007) (0)
Summarizing introductions and persistence using Markov jumps inferred by BEAST (2021) (0)
Fold or hold: experimental evolution in vitro (2013) (0)
Pandemics: spend on surveillance, not prediction (2018) (0)
Investigating the origin and nature of epidemics in the history of HIV-1 (2007) (0)
Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak (2018) (0)
Reconciling host and pathogen trees for a large HIV transmission chain (2013) (0)
Zika virus into the United States (2017) (0)
Publisher Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland (2021) (0)
Tracking virus outbreaks in the twenty-first century (2018) (0)
Edinburgh Research Explorer Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1 (2018) (0)
SARS-CoV-2 evolution during treatment of chronic infection (2021) (0)
Author response: Integrating influenza antigenic dynamics with molecular evolution (2013) (0)
Persistent HIV-1 replication maintains the tissue reservoir 1 during therapy 2 3 4 (2015) (0)
Edinburgh Research Explorer Integrating influenza antigenic dynamics with molecular evolution (2014) (0)
1 Temporal signal and the phylodynamic threshold of SARS-CoV-2 2 3 (2020) (0)
Quantifying the value of viral genomics when inferring who infected whom in the 2014–16 Ebola virus outbreak in Guinea (2023) (0)
Publisher Correction: Monitoring key epidemiological parameters of SARS-CoV-2 transmission (2022) (0)
Correction to: The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK (2022) (0)
Edinburgh Research Explorer Identification of common deletions in the spike protein of severe acute respiratory syndrome coronavirus 2 (2020) (0)
Nature Microbiology Review (2018) (0)
Evolutionary genetics and the emergence of SARS coronavirus. (2005) (0)
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis (2019) (0)
Inferring large-scale heterogeneous evolutionary processes through time (2013) (0)
Fold or die: experimental evolution in vitro (2012) (0)
Author Correction: Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland (2020) (0)
Tracing the emergence, transmission and adaptation of pandemic MRSA (2012) (0)
Reconstruction of an HIV Transmission History in a Bayesian Coalescent Framework (2013) (0)
Edinburgh Explorer Inferring heterogeneous evolutionary processes through time (2014) (0)
Title Spatial Dynamics of Human-Origin H 1 Influenza A Virus in NorthAmerican Swine (2011) (0)
Comparison of Eleven RNA Extraction Methods for Poliovirus Direct Molecular Detection in Stool Samples (2023) (0)
Explorer Toward a quantitative understanding of viral phylogeography (2017) (0)
Explorer The RNA Virus Database (2018) (0)
Toward a quantitative understan ding of viral phylogeography (2011) (0)
Publisher Correction: Monitoring key epidemiological parameters of SARS-CoV-2 transmission (2022) (0)
Real-time digital pathogen surveillance — the time is now (2015) (0)
ESTIMATING THE RATE OF INTER-SUBTYPE RECOMBINATION IN EARLY HIV-1 1 GROUP M STRAINS 2 (2012) (0)
ADVANCES IN PARASITOLOGY, VOL 54 (2003) (0)
For consideration as a Research Article (2010) (0)
Population genomic analysis of within-host HIV diversity (2007) (0)
Rapid and sensitive direct detection and identification of poliovirus from stool and 1 environmental surveillance samples using nanopore sequencing 2 (2020) (0)
Livestock Origin for a Human Pandemic Clone of Community-Associated Methicillin-Resistant <named-content content-type='genus-species'>Staphylococcus aureus</named-content> (2013) (0)
Efficient phylogeographic hypothesis testing in viral epidemic histories (2010) (0)
Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England (2022) (0)
Towards Realtime Bayesian Inference for Pathogen Phylodynamics (2019) (0)
Manuscript Type: Letter (2008) (0)
The evolution of gene overlap in RNA viruses (2008) (0)
Explorer Bayesian Phylogeography Finds Its Roots (2017) (0)
The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection (2023) (0)

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