SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference. - Dimitris Paraskevis; Koen Deforche; Philippe Lemey; Gkikas Magiorkinis; Angelos Hatzakis; Anne-Mieke Vandamme (Bioinform., 2005)

Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo. - Koen Deforche; Ricardo Camacho; Kristel Van Laethem; Beth Shapiro; Yves Moreau; Andrew Rambaut; Anne-Mieke Vandamme; Philippe Lemey (J. Comput. Biol., 2007)

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics. - Philippe Lemey; Sergei L. Kosakovsky Pond; Alexei J. Drummond; Oliver G. Pybus; Beth Shapiro; Helena Barroso; Nuno Taveira; Andrew Rambaut (PLoS Comput. Biol., 2007)

Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. - Koen Deforche; Ricardo Camacho; Kristel Van Laethem; Philippe Lemey; Andrew Rambaut; Yves Moreau; Anne-Mieke Vandamme (Bioinform., 2008)

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. - Philippe Lemey; Martin Lott; Darren P. Martin; Vincent Moulton (BMC Bioinform., 2009)

Bayesian Phylogeography Finds Its Roots. - Philippe Lemey; Andrew Rambaut; Alexei J. Drummond; Marc A. Suchard (PLoS Comput. Biol., 2009)

RDP3: a flexible and fast computer program for analyzing recombination. - Darren P. Martin; Philippe Lemey; Martin Lott; Vincent Moulton; David Posada; Pierre Lefeuvre (Bioinform., 2010)

Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape. - 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 (BMC Bioinform., 2010)

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. - Filip Bielejec; Andrew Rambaut; Marc A. Suchard; Philippe Lemey (Bioinform., 2011)

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. - Philippe Lemey; Vladimir N. Minin; Filip Bielejec; Sergei L. Kosakovsky Pond; Marc A. Suchard (Bioinform., 2012)

Reconstruction of an HIV Transmission History in a Bayesian Coalescent Framework. - Bram Vrancken; Andrew Rambaut; Guy Baele; Anne-Mieke Vandamme; Kristel Van Laethem; Eric Van Wijngaerden; Alexei J. Drummond; Marc A. Suchard; Philippe Lemey (IWBBIO, 2013)

Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency. - Guy Baele; Philippe Lemey (Bioinform., 2013)

Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution. - Guy Baele; Philippe Lemey; Stijn Vansteelandt (BMC Bioinform., 2013)

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios. - Filip Bielejec; Philippe Lemey; Luiz Carvalho; Guy Baele; Andrew Rambaut; Marc A. Suchard (BMC Bioinform., 2014)

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates. - 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 (PLoS Comput. Biol., 2014)

Global circulation patterns of seasonal influenza viruses vary with antigenic drift. - 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; et al. (Nat., 2015)

SERAPHIM: studying environmental rasters and phylogenetically informed movements. - Simon Dellicour; Rebecca Rose; Nuno R. Faria; Philippe Lemey; Oliver G. Pybus (Bioinform., 2016)

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST. - Guy Baele; Philippe Lemey; Andrew Rambaut; Marc A. Suchard (Bioinform., 2017)

Virus genomes reveal factors that spread and sustained the Ebola epidemic. - 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; et al. (Nat., 2017)

Bayesian Best-Arm Identification for Selecting Influenza Mitigation Strategies. - Pieter J. K. Libin; Timothy Verstraeten; Diederik M. Roijers; Jelena Grujic; Kristof Theys; Philippe Lemey; Ann Nowé (ECML/PKDD (3), 2018)

Deep Reinforcement Learning for Large-Scale Epidemic Control. - Pieter J. K. Libin; Arno Moonens; Timothy Verstraeten; Fabian Perez-Sanjines; Niel Hens; Philippe Lemey; Ann Nowé (ECML/PKDD (5), 2020)

Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region. - 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; et al. (Bioinform., 2020)

Massive Parallelization Boosts Big Bayesian Multidimensional Scaling. - Andrew J. Holbrook; Philippe Lemey; Guy Baele; Simon Dellicour; Dirk Brockmann; Andrew Rambaut; Marc A. Suchard (J. Comput. Graph. Stat., 2021)

Accelerating Bayesian inference of dependency between mixed-type biological traits. - Zhenyu Zhang; Akihiko Nishimura; Nídia S. Trovão; Joshua L. Cherry; Andrew J. Holbrook; Xiang Ji; Philippe Lemey; Marc A. Suchard (PLoS Comput. Biol., 2023)

Many-core algorithms for high-dimensional gradients on phylogenetic trees. - Karthik Gangavarapu; Xiang Ji; Guy Baele; Mathieu Fourment; Philippe Lemey; Frederick A. Matsen IV; Marc A. Suchard (Bioinform., 2024)