Philippe Lemey

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 11

Top Topics

Bayesian Inference

Top Venues

PLoS Comput. Biol.

Publications

Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A. Matsen IV, Marc A. Suchard
Many-core algorithms for high-dimensional gradients on phylogenetic trees. Bioinform. 40 (2) (2024)
Zhenyu Zhang, Akihiko Nishimura, Nídia S. Trovão, Joshua L. Cherry, Andrew J. Holbrook, Xiang Ji, Philippe Lemey, Marc A. Suchard
Accelerating Bayesian inference of dependency between mixed-type biological traits. PLoS Comput. Biol. 19 (8) (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)
Pieter J. K. Libin, Arno Moonens, Timothy Verstraeten, Fabian Perez-Sanjines, Niel Hens, Philippe Lemey, Ann Nowé
Deep Reinforcement Learning for Large-Scale Epidemic Control. ECML/PKDD (5) (2020)
Simon Dellicour, Philippe Lemey, Jean Artois, Tommy T. Lam, Alice Fusaro, Isabella Monne, Giovanni Cattoli, Dmitry Kuznetsov, Ioannis Xenarios, Gwenaelle Dauphin, Wantanee Kalpravidh, Sophie von Dobschütz, Filip Claes, Scott H. Newman, Marc A. Suchard, Guy Baele, Marius Gilbert
Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region. Bioinform. 36 (7) (2020)
Pieter Libin, Arno Moonens, Timothy Verstraeten, Fabian Perez-Sanjines, Niel Hens, Philippe Lemey, Ann Nowé
Deep reinforcement learning for large-scale epidemic control. CoRR (2020)
Pieter J. K. Libin, Timothy Verstraeten, Diederik M. Roijers, Jelena Grujic, Kristof Theys, Philippe Lemey, Ann Nowé
Bayesian Best-Arm Identification for Selecting Influenza Mitigation Strategies. ECML/PKDD (3) (2018)
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)
Pieter Libin, Timothy Verstraeten, Diederik M. Roijers, Jelena Grujic, Kristof Theys, Philippe Lemey, Ann Nowé
Bayesian Best-Arm Identification for Selecting Influenza Mitigation Strategies. CoRR (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)
Simon Dellicour, Rebecca Rose, Nuno R. Faria, Philippe Lemey, Oliver G. Pybus
SERAPHIM: studying environmental rasters and phylogenetically informed movements. Bioinform. 32 (20) (2016)
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)
Guy Baele, Philippe Lemey, Stijn Vansteelandt
Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution. BMC Bioinform. 14 (2013)
Guy Baele, Philippe Lemey
Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency. Bioinform. 29 (16) (2013)
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)
Philippe Lemey, Vladimir N. Minin, Filip Bielejec, Sergei L. Kosakovsky Pond, Marc A. Suchard
A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. Bioinform. 28 (24) (2012)
Filip Bielejec, Andrew Rambaut, Marc A. Suchard, Philippe Lemey
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinform. 27 (20) (2011)
Darren P. Martin, Philippe Lemey, Martin Lott, Vincent Moulton, David Posada, Pierre Lefeuvre
RDP3: a flexible and fast computer program for analyzing recombination. Bioinform. 26 (19) (2010)
Kristof Theys, Koen Deforche, Gertjan Beheydt, Yves Moreau, Kristel Van Laethem, Philippe Lemey, Ricardo Camacho, Soo-Yon Rhee, Robert W. Shafer, Eric Van Wijngaerden, Anne-Mieke Vandamme
Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. BMC Bioinform. 11 (2010)
Philippe Lemey, Andrew Rambaut, Alexei J. Drummond, Marc A. Suchard
Bayesian Phylogeography Finds Its Roots. PLoS Comput. Biol. 5 (9) (2009)
Philippe Lemey, Martin Lott, Darren P. Martin, Vincent Moulton
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinform. 10 (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)
Dimitris Paraskevis, Koen Deforche, Philippe Lemey, Gkikas Magiorkinis, Angelos Hatzakis, Anne-Mieke Vandamme
SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference. Bioinform. 21 (7) (2005)