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2020 – today
- 2023
[j28]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)- 2021
- [j27]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): 11-24 (2021)
2010 – 2019
- 2019
- [j26]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) - 2017
- [j25]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): 1798-1805 (2017) - [j24]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): 309-315 (2017) - [j23]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, Aluisio 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): 406-410 (2017) - [j22]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:
Lorenzo-Redondo et al. reply. Nat. 551(7681): E10-E10 (2017) - 2015
- [j21]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): 217-220 (2015) - [j20]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) - 2014
- [j19]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: 133 (2014) - [j18]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) - [j17]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) - 2013
- [c1]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: 555-556 - 2012
- [j16]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: 47 (2012) - 2011
- [j15]Filip Bielejec, Andrew Rambaut, Marc A. Suchard, Philippe Lemey:
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinform. 27(20): 2910-2912 (2011) - 2010
- [j14]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)
2000 – 2009
- 2009
- [j13]Marc A. Suchard, Andrew Rambaut:
Many-core algorithms for statistical phylogenetics. Bioinform. 25(11): 1370-1376 (2009) - [j12]Robert Belshaw, Tulio de Oliveira, Sidney Markowitz, Andrew Rambaut:
The RNA Virus Database. Nucleic Acids Res. 37(Database-Issue): 431-435 (2009) - [j11]Philippe Lemey, Andrew Rambaut, Alexei J. Drummond, Marc A. Suchard:
Bayesian Phylogeography Finds Its Roots. PLoS Comput. Biol. 5(9) (2009) - 2008
- [j10]Koen Deforche, Ricardo Camacho, Kristel Van Laethem, Philippe Lemey, Andrew Rambaut, Yves Moreau, Anne-Mieke Vandamme:
Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. Bioinform. 24(1): 34-41 (2008) - 2007
- [j9]Koen Deforche, Ricardo Camacho, Kristel Van Laethem, Beth Shapiro, Yves Moreau, Andrew Rambaut, Anne-Mieke Vandamme, Philippe Lemey:
Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo. J. Comput. Biol. 14(8): 1105-1114 (2007) - [j8]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) - 2002
- [j7]Oliver G. Pybus, Andrew Rambaut:
GENIE: estimating demographic history from molecular phylogenies. Bioinform. 18(10): 1404-1405 (2002) - 2000
- [j6]Andrew Rambaut:
Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinform. 16(4): 395-399 (2000)
1990 – 1999
- 1997
- [j5]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): 235-238 (1997) - [j4]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): 303-306 (1997) - [j3]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): 559-560 (1997) - 1996
- [j2]Andrew Rambaut, Nicholas C. Grassly, Sean Nee, Paul H. Harvey:
Bi-De: an application for simulating phylogenetic processes. Comput. Appl. Biosci. 12(6): 469-471 (1996) - 1995
- [j1]Andy Purvis, Andrew Rambaut:
Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Comput. Appl. Biosci. 11(3): 247-251 (1995)
Coauthor Index
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