Andrew Rambaut

Publication Activity (10 Years)

Years Active: 1995-2023
Publications (10 Years): 7

Top Topics

Multidimensional Scaling

Influenza Virus

Population Dynamics

Top Venues

PLoS Comput. Biol.

Publications

Rachel Colquhoun, Ben Jackson, Áine Niamh O'toole, Andrew Rambaut
SCORPIO: a utility for defining and classifying mutation constellations of virus genomes. Bioinform. 39 (10) (2023)
Andrew J. Holbrook, Philippe Lemey, Guy Baele, Simon Dellicour, Dirk Brockmann, Andrew Rambaut, Marc A. Suchard
Massive Parallelization Boosts Big Bayesian Multidimensional Scaling. J. Comput. Graph. Stat. 30 (1) (2021)
Remco R. Bouckaert, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, David A. Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, Alexei J. Drummond
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15 (4) (2019)
Guy Baele, Philippe Lemey, Andrew Rambaut, Marc A. Suchard
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST. Bioinform. 33 (12) (2017)
Nuno R. Faria, Joshua Quick, I. M. Claro, Julien Thézé, J. G. de Jesus, Marta Giovanetti, Moritz U. G. Kraemer, S. C. Hill, Allison Black, A. C. Da Costa, L. C. Franco, S. P. Silva, Chieh-Hsi Wu, Jayna Raghwani, Simon Cauchemez, Louis du Plessis, M. P. Verotti, W. K. de Oliveira, E. H. Carmo, G. E. Coelho, A. C. F. S. Santelli, L. C. Vinhal, C. M. Henriques, J. T. Simpson, Matthew Loose, Kristian G. Andersen, N. D. Grubaugh, S. Somasekar, C. Y. Chiu, J. E. Muñoz-Medina, C. R. Gonzalez-Bonilla, Carolina Fócil Arias, L. L. Lewis-Ximenez, S. A. Baylis, A. O. Chieppe, S. F. Aguiar, C. A. Fernandes, P. S. Lemos, B. L. S. Nascimento, H. A. O. Monteiro, I. C. Siqueira, M. G. de Queiroz, T. R. de Souza, J. F. Bezerra, M. R. Lemos, G. F. Pereira, D. Loudal, L. C. Moura, R. Dhalia, R. F. França, T. Magalhães, E. T. Marques Jr, Thomas Jaenisch, Gabriel da Luz Wallau, M. C. de Lima, V. Nascimento, E. M. de Cerqueira, M. M. de Lima, D. L. Mascarenhas, J. P. Moura Neto, A. S. Levin, T. R. Tozetto-Mendoza, S. N. Fonseca, M. C. Mendes-Correa, F. P. Milagres, A. Segurado, Edward C. Holmes, Andrew Rambaut, Trevor Bedford, M. R. T. Nunes, Ester C. Sabino, Luis Carlos Alcantara, Nicholas J. Loman, Oliver G. Pybus
Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nat. 546 (7658) (2017)
Ramon Lorenzo-Redondo, Helen R. Fryer, Trevor Bedford, Eun-Young Kim, John A. C. Archer, Sergei L. Kosakovsky Pond, Yoon-Seok Chung, Sudhir Penugonda, Jeffrey G. Chipman, Courtney V. Fletcher, Timothy W. Schacker, Michael H. Malim, Andrew Rambaut, Ashley T. Haase, Angela R. McLean, Steven M. Wolinsky
. reply. Nat. 551 (7681) (2017)
Gytis Dudas, Luiz Max Carvalho, Trevor Bedford, Andrew J. Tatem, Guy Baele, Nuno R. Faria, Daniel J. Park, Jason T. Ladner, Armando Arias, Danny Asogun, Filip Bielejec, Sarah L. Caddy, Matthew Cotten, Jonathan D'Ambrozio, Simon Dellicour, Antonino Di Caro, Joseph W. Diclaro, Sophie Duraffour, Michael J. Elmore, Lawrence S. Fakoli, Ousmane Faye, Merle L. Gilbert, Sahr M. Gevao, Stephen Gire, Adrianne Gladden-Young, Andreas Gnirke, Augustine Goba, Donald S. Grant, Bart L. Haagmans, Julian A. Hiscox, Umaru Jah, Jeffrey R. Kugelman, Di Liu, Jia Lu, Christine M. Malboeuf, Suzanne Mate, David A. Matthews, Christian B. Matranga, Luke W. Meredith, James Qu, Joshua Quick, Suzan D. Pas, My V. T. Phan, Georgios Pollakis, Chantal B. Reusken, Mariano Sanchez-Lockhart, Stephen F. Schaffner, John S. Schieffelin, Rachel S. G. Sealfon, Etienne Simon-Loriere, Saskia L. Smits, Kilian Stoecker, Lucy Thorne, Ekaete Alice Tobin, Mohamed A. Vandi, Simon J. Watson, Kendra West, Shannon Whitmer, Michael R. Wiley, Sarah M. Winnicki, Shirlee Wohl, Roman Wölfel, Nathan L. Yozwiak, Kristian G. Andersen, Sylvia O. Blyden, Fatorma Bolay, Miles W. Carroll, Bernice Dahn, Boubacar Diallo, Pierre Formenty, Christophe Fraser, George F. Gao, Robert F. Garry, Ian Goodfellow, Stephan Günther, Christian T. Happi, Edward C. Holmes, Brima Kargbo, Sakoba Keïta, Paul Kellam, Marion Koopmans, Jens H. Kuhn, Nicholas J. Loman, N'Faly Magassouba, Dhamari Naidoo, Stuart T. Nichol, Tolbert Nyenswah, Gustavo F. Palacios, Oliver G. Pybus, Pardis C. Sabeti, Amadou Sall, Ute Ströher, Isatta Wurie, Marc A. Suchard, Philippe Lemey, Andrew Rambaut
Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nat. 544 (7650) (2017)
Matthew Hall, Mark E. J. Woolhouse, Andrew Rambaut
Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set. PLoS Comput. Biol. 11 (12) (2015)
Trevor Bedford, Steven Riley, Ian G. Barr, Shobha Broor, Mandeep Chadha, Nancy J. Cox, Rodney S. Daniels, C. Palani Gunasekaran, Aeron C. Hurt, Anne Kelso, Alexander Klimov, Nicola S. Lewis, Xiyan Li, John W. McCauley, Takato Odagiri, Varsha Potdar, Andrew Rambaut, Yuelong Shu, Eugene Skepner, Derek J. Smith, Marc A. Suchard, Masato Tashiro, Dayan Wang, Xiyan Xu, Philippe Lemey, Colin A. Russell
Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nat. 523 (7559) (2015)
Bram Vrancken, Andrew Rambaut, Marc A. Suchard, Alexei J. Drummond, Guy Baele, Inge Derdelinckx, Eric Van Wijngaerden, Anne-Mieke Vandamme, Kristel Van Laethem, Philippe Lemey
The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates. PLoS Comput. Biol. 10 (4) (2014)
Filip Bielejec, Philippe Lemey, Luiz Carvalho, Guy Baele, Andrew Rambaut, Marc A. Suchard
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. BMC Bioinform. 15 (2014)
Remco R. Bouckaert, Joseph Heled, Denise Kühnert, Timothy G. Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, Alexei J. Drummond
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Comput. Biol. 10 (4) (2014)
Bram Vrancken, Andrew Rambaut, Guy Baele, Anne-Mieke Vandamme, Kristel Van Laethem, Eric Van Wijngaerden, Alexei J. Drummond, Marc A. Suchard, Philippe Lemey
Reconstruction of an HIV Transmission History in a Bayesian Coalescent Framework. IWBBIO (2013)
John P. Archer, Greg Baillie, Simon J. Watson, Paul Kellam, Andrew Rambaut, David L. Robertson
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinform. 13 (2012)
Filip Bielejec, Andrew Rambaut, Marc A. Suchard, Philippe Lemey
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinform. 27 (20) (2011)
John P. Archer, Andrew Rambaut, Bruce E. Taillon, P. Richard Harrigan, Marilyn Lewis, David L. Robertson
The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time - An Ultra-Deep Approach. PLoS Comput. Biol. 6 (12) (2010)
Robert Belshaw, Tulio de Oliveira, Sidney Markowitz, Andrew Rambaut
The RNA Virus Database. Nucleic Acids Res. 37 (Database-Issue) (2009)
Marc A. Suchard, Andrew Rambaut
Many-core algorithms for statistical phylogenetics. Bioinform. 25 (11) (2009)
Philippe Lemey, Andrew Rambaut, Alexei J. Drummond, Marc A. Suchard
Bayesian Phylogeography Finds Its Roots. PLoS Comput. Biol. 5 (9) (2009)
Koen Deforche, Ricardo Camacho, Kristel Van Laethem, Philippe Lemey, Andrew Rambaut, Yves Moreau, Anne-Mieke Vandamme
fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. Bioinform. 24 (1) (2008)
Philippe Lemey, Sergei L. Kosakovsky Pond, Alexei J. Drummond, Oliver G. Pybus, Beth Shapiro, Helena Barroso, Nuno Taveira, Andrew Rambaut
Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics. PLoS Comput. Biol. 3 (2) (2007)
Koen Deforche, Ricardo Camacho, Kristel Van Laethem, Beth Shapiro, Yves Moreau, Andrew Rambaut, Anne-Mieke Vandamme, Philippe Lemey
. J. Comput. Biol. 14 (8) (2007)
Oliver G. Pybus, Andrew Rambaut
GENIE: estimating demographic history from molecular phylogenies. Bioinform. 18 (10) (2002)
Andrew Rambaut
Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinform. 16 (4) (2000)
Andrew Rambaut, Paul H. Harvey, Sean Nee
End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences. Comput. Appl. Biosci. 13 (3) (1997)
Nicholas C. Grassly, Jun Adachi, Andrew Rambaut
PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13 (5) (1997)
Andrew Rambaut, Nicholas C. Grassly
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13 (3) (1997)
Andrew Rambaut, Nicholas C. Grassly, Sean Nee, Paul H. Harvey
Bi-De: an application for simulating phylogenetic processes. Comput. Appl. Biosci. 12 (6) (1996)
A. Purvis, Andrew Rambaut
Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Comput. Appl. Biosci. 11 (3) (1995)