Philippe Lemey

发表

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates

Guy Baele, Anne-Mieke Vandamme, Alexei J. Drummond, 2014, PLoS Comput. Biol..

Inferring Heterogeneous Evolutionary Processes Through Time: from Sequence Substitution to Phylogeography

Guy Baele, Marc A. Suchard, Andrew Rambaut, 2013, Systematic biology.

The Phylogenetic Handbook: Multiple sequence alignment

Des Higgins, Philippe Lemey, Des Higgins, 2009 .

RDP3: a flexible and fast computer program for analyzing recombination

Vincent Moulton, David Posada, Philippe Lemey, 2010, Bioinform..

Estimating the Relative Contribution of dNTP Pool Imbalance and APOBEC3G/3F Editing to HIV Evolution In Vivo

Yves Moreau, Anne-Mieke Vandamme, Beth Shapiro, 2007, J. Comput. Biol..

Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency

Guy Baele, Philippe Lemey, P. Lemey, 2013, Bioinform..

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Daniel L. Ayres, Guy Baele, Marc A Suchard, 2018, Virus evolution.

Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape

Yves Moreau, Kristof Theys, Anne-Mieke Vandamme, 2009, BMC Bioinformatics.

Reconstruction of an HIV Transmission History in a Bayesian Coalescent Framework

Guy Baele, Anne-Mieke Vandamme, Alexei J. Drummond, 2013, IWBBIO.

Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements

Lam Si Tung Ho, Marc A. Suchard, Philippe Lemey, 2019, Journal of the American Statistical Association.

πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios

Guy Baele, Marc A. Suchard, Andrew Rambaut, 2013, BMC Bioinformatics.

Global circulation patterns of seasonal influenza viruses vary with antigenic drift

Trevor Bedford, Colin A. Russell, Derek J. Smith, 2015, Nature.

Accurate model selection while accommodating phylogenetic uncertainty in Bayesian phylogenetics

Guy Baele, Philippe Lemey, 2012 .

Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates.

Marc A Suchard, Philippe Lemey, Mandev S Gill, 2016, Systematic biology.

Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment

Yves Moreau, Anne-Mieke Vandamme, Ricardo Camacho, 2008, Bioinform..

SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference

Anne-Mieke Vandamme, Philippe Lemey, Koen Deforche, 2005, Bioinform..

Bayesian Best-Arm Identification for Selecting Influenza Mitigation Strategies pdf

Ann Nowé, Pieter Libin, Timothy Verstraeten, 2017, ECML/PKDD.

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection

Vladimir N. Minin, Sergei L. Kosakovsky Pond, Marc A. Suchard, 2012, Bioinform..

Bayesian Phylogeography Finds Its Roots

Alexei J. Drummond, Marc A. Suchard, Andrew Rambaut, 2009, PLoS Comput. Biol..

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

Marc A. Suchard, Andrew Rambaut, Philippe Lemey, 2011, Bioinform..

Adaptive MCMC for multi-partite data in Bayesian Phylogenetics

Guy Baele, Marc A. Suchard, Andrew Rambaut, 2018 .

SERAPHIM: studying environmental rasters and phylogenetically informed movements

Rebecca Rose, Philippe Lemey, Oliver G. Pybus, 2016, Bioinform..

Reconstructing the initial global spread of a human influenza pandemic

Andrew Rambaut, Philippe Lemey, Marc Suchard, 2017 .

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

Sergei L. Kosakovsky Pond, Beth Shapiro, Alexei J. Drummond, 2007, PLoS Comput. Biol..

Massive Parallelization Boosts Big Bayesian Multidimensional Scaling

Dirk Brockmann, Andrew Rambaut, Philippe Lemey, 2019, J. Comput. Graph. Stat..

Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution

Guy Baele, Stijn Vansteelandt, Philippe Lemey, 2013, BMC Bioinformatics.

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST

Guy Baele, Marc A. Suchard, Andrew Rambaut, 2017, Bioinform..

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning

Vincent Moulton, Philippe Lemey, Darren P. Martin, 2009, BMC Bioinformatics.

Ebola is ook ons probleem

P. Van Damme, Hans Keune, Niko Speybroeck, 2014 .

Virus genomes reveal factors that spread and sustained the Ebola epidemic

Trevor Bedford, George F. Gao, Andrew J. Tatem, 2017, Nature.

Shrinkage-based random local clocks with scalable inference

Xiang Ji, Marc A. Suchard, Philippe Lemey, 2021, 2105.07119.

Principled, practical, flexible, fast: A new approach to phylogenetic factor analysis

Guy Baele, Marc A. Suchard, Andrew J. Holbrook, 2021, Methods in ecology and evolution.

Scalable Bayesian divergence time estimation with ratio transformations.

Guy Baele, Marc A. Suchard, Jeffrey L. Thorne, 2021, Systematic biology.

Hamiltonian zigzag speeds up large-scale learning of direct eﬀects among mixed-type biological traits

Marc A. Suchard, Philippe Lemey, Zhenyu Zhang, 2022 .

Efficient Bayesian inference of general Gaussian models on large phylogenetic trees

Guy Baele, Marc A Suchard, Lam Si Tung Ho, 2020, The Annals of Applied Statistics.

Data from: Integrating influenza antigenic dynamics with molecular evolution

Trevor Bedford, Colin A. Russell, Marc A. Suchard, 2014 .

Identifying predictors of time-inhomogeneous viral evolutionary processes

Guy Baele, Allen G. Rodrigo, Marc A. Suchard, 2016, Virus evolution.

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Christina Boucher, Olivier Gascuel, Guy Baele, 2020, Proceedings of the National Academy of Sciences.

Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing

Guy Baele, Anne-Mieke Vandamme, Bram Vrancken, 2016, Viruses.

Virus evolution and transmission in an ever more connected world

Andrew J. Tatem, Philippe Lemey, Oliver G. Pybus, 2015, Proceedings of the Royal Society B: Biological Sciences.

Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting

Christl A. Donnelly, Simon Cauchemez, Edward C. Holmes, 2016, PLoS pathogens.

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

Daniel L. Ayres, Guy Baele, Marc A Suchard, 2019, Systematic biology.

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics

Erik Axelsson, Beth Shapiro, M. Thomas P. Gilbert, 2010, Proceedings of the National Academy of Sciences.

The Phylogenetic Handbook: Index

Anne-Mieke Vandamme, Philippe Lemey, Marco Salemi, 2009 .

Estimating an In Vivo Fitness Landscape During Protease and Reverse Transcriptase Treatment from Observed Genetic Evolution to Predict Accumulation of Mutations under Selective Pressure

Yves Moreau, Kristof Theys, Anne-Mieke Vandamme, 2007 .

Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline

John J. Welch, Beth Shapiro, Marc A. Suchard, 2011, Current Biology.

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

Guy Baele, Marc A Suchard, Andrew Rambaut, 2018, Nature Communications.

Three roads diverged? Routes to phylogeographic inference.

Marc A Suchard, Philippe Lemey, M. Suchard, 2010, Trends in ecology & evolution.

Evolutionary Dynamics of Human Rotaviruses: Balancing Reassortment with Preferred Genome Constellations

Jelle Matthijnssens, Philippe Lemey, Sarah M. McDonald, 2009, PLoS pathogens.

Emerging Concepts of Data Integration in Pathogen Phylodynamics

Guy Baele, Marc A. Suchard, Andrew Rambaut, 2016, Systematic biology.

Genetic Variability and Molecular Evolution of the Human Respiratory Syncytial Virus Subgroup B Attachment G Protein

Anne-Mieke Vandamme, Philippe Lemey, Marc Van Ranst, 2005, Journal of Virology.

ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL.

Trevor Bedford, Marc A Suchard, Philippe Lemey, 2014, The annals of applied statistics.

A genotypic resistance assay for the detection of drug resistance in the human immunodeficiency virus type 1 envelope gene.

Anne-Mieke Vandamme, Philippe Lemey, Yoeri Schrooten, 2005, Journal of virological methods.

Graph hierarchies for phylogeography

Marc A Suchard, Philippe Lemey, Janet S Sinsheimer, 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

Integrating influenza antigenic dynamics with molecular evolution

Trevor Bedford, Marc A Suchard, Andrew Rambaut, 2013, eLife.

Unifying the spatial epidemiology and molecular evolution of emerging epidemics

Forrest W. Crawford, Marc A. Suchard, Andrew Rambaut, 2012, Proceedings of the National Academy of Sciences.

Gradients do grow on trees: a linear-time 𝒪 (N)-dimensional gradient for statistical phylogenetics.

Xiang Ji, Guy Baele, Marc A Suchard, 2020, Molecular biology and evolution.

The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia

Guy Baele, Marc A. Suchard, Bram Vrancken, 2017, Scientific Reports.

Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation

Guy Baele, Marc A. Suchard, Philippe Lemey, 2016, Microbial genomics.

Limitations to contact tracing and phylogenetic analysis in establishing HIV type 1 transmission networks in Cuba.

Anne-Mieke Vandamme, Philippe Lemey, Sonia Resik, 2007, AIDS research and human retroviruses.

Bayesian Inference Reveals Host-Specific Contributions to the Epidemic Expansion of Influenza A H5N1.

Guy Baele, Marius Gilbert, Marc A Suchard, 2015, Molecular biology and evolution.

The global antigenic diversity of swine influenza A viruses

Tavis K. Anderson, Paul Kellam, Takehiko Saito, 2016, eLife.

Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints

Marc A Suchard, Andrew Rambaut, Philippe Lemey, 2013, Philosophical Transactions of the Royal Society B: Biological Sciences.

Spatial Dynamics of Human-Origin H1 Influenza A Virus in North American Swine

Cécile Viboud, Marc A. Suchard, Edward C. Holmes, 2011, PLoS pathogens.

Spatio‐temporal analysis of Nova virus, a divergent hantavirus circulating in the European mole in Belgium

Lies Laenen, Philippe Lemey, Simon Dellicour, 2016, Molecular ecology.

Time-measured phylogenies of gag, pol and env sequence data reveal the direction and time interval of HIV-1 transmission

Philippe Lemey, Hanneke Schuitemaker, P. Lemey, 2011, AIDS.

Relaxed Random Walks at Scale.

Xiang Ji, Marc A Suchard, Philippe Lemey, 2019, Systematic biology.

The coalescent: population genetic inference using genealogies

Anne-Mieke Vandamme, Allen G. Rodrigo, Philippe Lemey, 2009 .

Phylogeography and population dynamics of dengue viruses in the Americas.

Marc A Suchard, Andrew J Tatem, Andrew Rambaut, 2012, Molecular biology and evolution.

Recent advances in computational phylodynamics.

Guy Baele, Marc A Suchard, Bram Vrancken, 2018, Current opinion in virology.

Exceptional Heterogeneity in Viral Evolutionary Dynamics Characterises Chronic Hepatitis C Virus Infection

Marc A Suchard, Rebecca Rose, Philippe Lemey, 2016, PLoS pathogens.

Evolution and epidemic spread of SARS-CoV-2 in Brazil

Samir Bhatt, Maria Luiza Moretti, Andrew Rambaut, 2020, Science.

Genetic variation in mother–child acute seroconverter pairs from Zambia

Charles Wood, Philippe Lemey, P. Lemey, 2008, AIDS.

Global migration of influenza A viruses in swine

Cécile Viboud, Amy L. Vincent, Marc A. Suchard, 2015, Nature Communications.

Deep reinforcement learning for large-scale epidemic control

Timothy Verstraeten, Niel Hens, Philippe Lemey, 2020, ECML/PKDD.

Toward a quantitative understanding of viral phylogeography.

Marc A Suchard, Andrew Rambaut, Philippe Lemey, 2011, Current opinion in virology.

Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution

Trevor Bedford, Marc A Suchard, Andrew Rambaut, 2015, Methods in ecology and evolution.

Combining phylogeography and spatial epidemiology to uncover predictors of H5N1 influenza A virus diffusion

Rachel Beard, Matthew Scotch, Marc A. Suchard, 2014, Archives of Virology.

The emergence of SARS-CoV-2 in Europe and North America

Joel O. Wertheim, Michael Worobey, Marc A. Suchard, 2020, Science.

U.S. Human Immunodeficiency Virus Type 1 Epidemic: Date of Origin, Population History, and Characterization of Early Strains

Anne-Mieke Vandamme, Philippe Lemey, Oliver G. Pybus, 2003, Journal of Virology.

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Andrew Rambaut, David L Robertson, Xiaowei Jiang, 2020, Nature Microbiology.

Host ecology determines the dispersal patterns of a plant virus

Guy Baele, Marc A. Suchard, Bram Vrancken, 2015, Virus evolution.

Molecular Evolution and Circulation Patterns of Human Respiratory Syncytial Virus Subgroup A: Positively Selected Sites in the Attachment G Glycoprotein

Anne-Mieke Vandamme, Philippe Lemey, Marc Van Ranst, 2004, Journal of Virology.

The Phylogenetic Handbook: Introduction to recombination detection

David Posada, Philippe Lemey, 2009 .

The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing

Anne-Mieke Vandamme, Philippe Lemey, Marco Salemi, 2009 .

Reconstructing the History of Maize Streak Virus Strain A Dispersal To Reveal Diversification Hot Spots and Its Origin in Southern Africa

Edward P. Rybicki, Philippe Lemey, Darren P. Martin, 2011, Journal of Virology.

Using Viral Gene Sequences to Compare and Explain the Heterogeneous Spatial Dynamics of Virus Epidemics

Marius Gilbert, Rebecca Rose, Philippe Lemey, 2017, Molecular biology and evolution.

Recombination Confounds the Early Evolutionary History of Human Immunodeficiency Virus Type 1: Subtype G Is a Circulating Recombinant Form

Anne-Mieke Vandamme, Andrew Rambaut, Philippe Lemey, 2007, Journal of Virology.

Tracing the origin and history of the HIV-2 epidemic

Anne-Mieke Vandamme, Philippe Lemey, Marco Salemi, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Reconstructing the initial global spread of a human influenza pandemic: A Bayesian spatial-temporal model for the global spread of H1N1pdm.

Andrew Rambaut, Philippe Lemey, Marc Suchard, 2009, PLoS currents.