Author
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
12 papers
Recent·Most cited
L. A. Featherstone, A. Rambaut, S. Duchene, W. Wirth
Clockor2 is a web application for RTT regression that fits global and local molecular clocks, handling large datasets efficiently while keeping data on the client-side.
bioRxiv · Jul 13, 2023Evolutionary Biology
J. McBroome, A. de Bernardi Schneider, C. Roemer, M. T. Wolfinger, A. S. Hinrichs, A. N. O'Toole, C. Ruis, Y. Turakhia, A. Rambaut, R. Corbett-Detig
The paper introduces an automated method for pathogen lineage designation using phylogenetic trees, offering a consistent alternative to manual curation.
bioRxiv · Feb 3, 2023 · PreprintEvolutionary Biology
A. N. O'Toole, R. Neher, N. Ndodo, V. Borges, B. Gannon, J. P. Gomes, N. Groves, D. J. King, D. Maloney, P. Lemey, K. Lewandowski, N. Loman, R. Myers, M. A. Suchard, M. Worobey, , A. Rambaut
The paper analyzes MPXV genomes to show evidence of APOBEC3 deaminase editing, suggesting sustained human transmission since 2016.
bioRxiv · Jan 23, 2023 · PreprintEvolutionary Biology
N. D. Ndodo, J. Ashcroft, K. Lewandowski, A. Yinka-Ogunleye, C. Chukwu, A. Ahmad, D. King, A. Akinpelu, C. Maluquer de Motes, P. Ribeca, R. P. Sumner, A. Rambaut, M. Chester, T. Maishman, O. Bamidele, , D. Ulaeto
The paper identifies multiple coexisting Mpox lineages circulating in humans in Nigeria prior to the 2022 global outbreak, showing sustained human-to-human transmission and genetic changes.
bioRxiv · Jan 3, 2023 · PreprintMicrobiology
V. Hill, L. du Plessis, T. P. A. Peacock, D. Aggarwal, A. Carabelli, R. Colquhoun, N. Ellaby, E. Gallagher, N. Groves, B. Jackson, J. McCrone, A. N. O'Toole, A. Price, T. Sanderson, E. Scher, , A. Rambaut
This study investigates the origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 (Alpha) in the UK, finding that a chronically-infected immunocompetent individual likely drove its rapid mutation and spread.
bioRxiv · Mar 8, 2022Evolutionary Biology
E. C. Thomson, L. E. Rosen, J. G. Shepherd, R. Spreafico, A. da Silva Filipe, J. A. Wojcechowskyj, C. Davis, L. Piccoli, D. J. Pascall, J. Dillen, S. Lytras, N. Czudnochowski, R. Shah, M. Meury, N. Jesudason, , J. Nichols
The paper shows the N439K SARS-CoV-2 spike variant maintains replication fitness while evading antibody neutralization.
bioRxiv · Nov 4, 2020Microbiology
P. Lemey, S. Hong, V. Hill, G. Baele, C. Poletto, V. Colizza, A. O'Toole, J. T. McCrone, K. G. Andersen, M. Worobey, M. I. Nelson, A. Rambaut, M. A. Suchard
This paper integrates travel history data into Bayesian phylogeographic analysis of SARS-CoV-2 to improve virus spread reconstructions and address sampling bias.
bioRxiv · Jun 22, 2020 · PreprintEvolutionary Biology
S. Duchene, L. Featherstone, M. Haritopoulou-Sinanidou, A. Rambaut, P. Lemey, G. Baele
This study assesses the phylodynamic threshold of SARS-CoV-2 by analyzing genome sequences over time to determine when reliable evolutionary rate and outbreak timing estimates became possible.
bioRxiv · May 4, 2020Evolutionary Biology
A. G. Shaw, M. Majumdar, C. Troman, A. O'Toole, B. Benny, D. Abraham, I. Praharaj, G. Kang, S. Sharif, M. M. Alam, S. Shaukat, M. Angez, A. Khurshid, N. Mahmood, Y. Arshad, , N. C. Grassly
This paper presents a nested PCR and nanopore sequencing protocol for rapid and sensitive detection and identification of poliovirus in stool and environmental samples, reducing the time compared to traditional cell-culture methods.
bioRxiv · Apr 27, 2020Microbiology
A. Rambaut, E. C. Holmes, V. Hill, A. OToole, J. McCrone, C. Ruis, L. du Plessis, O. Pybus
This paper proposes a dynamic nomenclature system for SARS-CoV-2 to improve genomic epidemiology by tracking active lineages and their spread.
bioRxiv · Apr 17, 2020Microbiology
M. F. Boni, P. Lemey, X. Jiang, T. T.-Y. Lam, B. Perry, T. Castoe, A. Rambaut, D. L. Robertson
This paper estimates the divergence date of SARS-CoV-2 from its bat reservoir to be between 1948 and 1982, identifies non-recombinant regions for phylogenetic analysis, and highlights the role of horseshoe bats in viral emergence.
bioRxiv · Mar 30, 2020Evolutionary Biology
R. Bouckaert, T. G. Vaughan, J. Barido-Sottani, S. Duchene, M. Fourment, A. Gavryushkina, J. Heled, G. Jones, D. Kuhnert, N. de Maio, M. Matschiner, F. K. Mendes, N. Muller, H. A. Ogilvie, L. du Plessis, , A. J. Drummond
The paper describes new developments in the BEAST 2.5 software platform for Bayesian evolutionary analysis, expanding joint inference over multiple data types and complex phylodynamics.
bioRxiv · Nov 19, 2018Evolutionary Biology