List of works by Philippe Lemey

1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America

scientific article (publication date: 26 October 2016)

A comparative study of HIV-1 clade C env evolution in a Zambian infant with an infected rhesus macaque during disease progression

scientific article

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

scientific article published on 12 October 2012

A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue

scientific article published on 19 May 2020

A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses

scientific article

APOBEC3 deaminase editing in mpox virus as evidence for sustained human transmission since at least 2016

scientific article published on 02 November 2023

ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL. ⬇️

scientific article published on June 2015

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

scientific article published on 09 October 2020

Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study

scientific article published on 23 June 2020

Accurate model selection of relaxed molecular clocks in bayesian phylogenetics

scientific article published on 22 October 2012

Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling.

scientific article published on July 2017

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

scientific article

Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil

scientific article

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

scientific article (publication date: 23 March 2010)

Ancient hybridization and an Irish origin for the modern polar bear matriline

scientific article

Ancient papillomavirus-host co-speciation in Felidae

scientific article (publication date: 2007)

Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic

scientific article published on 10 May 2022

Are hepatitis B virus "subgenotypes" defined accurately?

scientific article published on 13 February 2010

Assessing the role of live poultry trade in community-structured transmission of avian influenza in China

scientific article published on 02 March 2020

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

scientific article published on 21 October 2019

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

scientific article published on 3 September 2015

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

scientific article

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.

scientific article published in January 2018

Bayesian phylogeography finds its roots

scientific article

Characterization of a putative ancestor of coxsackievirus B5.

scientific article

Circulation of HRSV in Belgium: from multiple genotype circulation to prolonged circulation of predominant genotypes

scientific article

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

scientific article

Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa

scientific article published on 01 July 2019

Complete genome sequence of Montana Myotis leukoencephalitis virus, phylogenetic analysis and comparative study of the 3' untranslated region of flaviviruses with no known vector

scientific article published in August 2002

Complete genome sequence, taxonomic assignment, and comparative analysis of the untranslated regions of the Modoc virus, a flavivirus with no known vector

scientific article published on February 2002

Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event

scientific article

Contribution of Epidemiological Predictors in Unraveling the Phylogeographic History of HIV-1 Subtype C in Brazil

scientific article

Correction: Geographic and Temporal Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted HIV-1 Drug Resistance: An Individual-Patient- and Sequence-Level Meta-Analysis

scientific article

Determinants of dengue virus dispersal in the Americas

scientific article published on 01 July 2020

Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa

scientific article published on 06 December 2019

Divergence dating using mixed effects clock modelling: An application to HIV-1

scientific article published on 01 July 2019

Ecuador Paraiso Escondido Virus, a New Flavivirus Isolated from New World Sand Flies in Ecuador, Is the First Representative of a Novel Clade in the Genus Flavivirus

scientific article

Emergence in Japan of an HIV-1 variant associated with transmission among men who have sex with men (MSM) in China: first indication of the International Dissemination of the Chinese MSM lineage

scientific article published on 30 January 2013

Emergence of primary NNRTI resistance mutations without antiretroviral selective pressure in a HAART-treated child

scientific article

Emerging Concepts of Data Integration in Pathogen Phylodynamics ⬇️

scientific article

Endogenous viral elements in shrew genomes provide insights into <i>Pestivirus</i> ancient history

scientific article published in 2022

Enzootic transmission of yellow fever virus, Venezuela

scientific article

Epidemiological history and genomic characterization of non-D1 HBV strains identified in Iran

scientific article published on 17 December 2014

Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework

scientific article published on 06 November 2020

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

scientific article

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

preprint article published on 12 June 2020

Evolutionary analysis of HBV "S" antigen genetic diversity in Iranian blood donors: a nationwide study

scientific article published on 22 October 2013

Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations

scientific article

Evolutionary history of the closely related group 2 coronaviruses: porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus OC43

scientific article published on July 2006

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

scientific article published on 28 July 2020

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

scientific article (publication date: September 2016)

Generalized linear models for identifying predictors of the evolutionary diffusion of viruses

scientific article

Genetic history of hepatitis C virus in East Asia

scientific article

Genetic variability among complete human respiratory syncytial virus subgroup A genomes: bridging molecular evolutionary dynamics and epidemiology

scientific article published in 2012

Genetic variability and molecular evolution of the human respiratory syncytial virus subgroup B attachment G protein

scientific article

Genome-Wide Evolutionary Analyses of G1P[8] Strains Isolated Before and After Rotavirus Vaccine Introduction

scientific article

Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation

scientific article

Genomic and epidemiological monitoring of yellow fever virus transmission potential

scientific article published in Science

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

scientific article published on 20 July 2023

Genomic characterization of novel dolphin papillomaviruses provides indications for recombination within the Papillomaviridae

scientific article published on 24 June 2008

Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature

scientific article published on 27 September 2021

Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis

scientific article

Global circulation patterns of seasonal influenza viruses vary with antigenic drift

scientific article published on 8 June 2015

Graph hierarchies for phylogeography

scientific article published on 04 February 2013

HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations

scientific article

HIV evolutionary dynamics within and among hosts

scientific article

HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification

scientific article published on 01 July 2020

High GUD incidence in the early 20 century created a particularly permissive time window for the origin and initial spread of epidemic HIV strains

scientific article

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

scientific article

Identifying the patterns and drivers of enzootic dynamics using reservoir sampling

scientific article published on 01 January 2019

Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models

scientific article

Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci

scientific article (publication date: March 2013)

In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography

scientific article published on 05 February 2020

Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements

scientific article published in 2020

Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography

scientific article

Integrating influenza antigenic dynamics with molecular evolution

scientific article

International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology

scientific article published in October 2013

Investigating the Origin and Spread of Hepatitis C Virus Genotype 5a

scientific article (publication date: May 2006)

Isolation and cloning of the raccoon (Procyon lotor) papillomavirus type 1 by using degenerate papillomavirus-specific primers

scientific article published on July 2005

Limited evolution of the yellow fever virus 17d in a mouse infection model

scientific article published on 01 January 2019

Longitudinal Genetic Characterization Reveals That Cell Proliferation Maintains a Persistent HIV Type 1 DNA Pool During Effective HIV Therapy

scientific article

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

scientific article

Mapping the origins and expansion of the Indo-European language family

scientific article

Measles virus and rinderpest virus divergence dated to the sixth century BCE

scientific article published on 01 June 2020

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

scientific article published on 01 January 2019

Molecular characterization of hepatitis B virus (HBV) strains circulating in the northern coast of the Persian Gulf and its comparison with worldwide distribution of HBV subgenotype D1.

scientific article published on 14 February 2014

Molecular characterization of hepatitis B virus strains circulating in Belgian patients co-infected with HIV and HBV: overt and occult infection

scientific article published in November 2011

Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication

scientific article

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents

scientific article published on 09 April 2021

Molecular evolutionary analysis and mutational pattern of full-length genomes of hepatitis B virus isolated from Belgian patients with different clinical manifestations

scientific article published in March 2010

New insights into flavivirus evolution, taxonomy and biogeographic history, extended by analysis of canonical and alternative coding sequences

scientific article

Novel hepatitis B virus subgenotype A6 in African-Belgian patients

scientific article published on 25 October 2009

On the biogeography of Centipeda: a species-tree diffusion approach

scientific article (publication date: March 2014)

On the importance of negative controls in viral landscape phylogeography

scientific article published on 01 July 2018

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

scientific article

Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants

scientific article

Phylodynamics and human-mediated dispersal of a zoonotic virus

scientific article (publication date: 28 October 2010)

Phylodynamics of H5N1 avian influenza virus in Indonesia

scientific article published on 11 May 2012

Phylogenetic analysis of hepatitis B virus full-length genomes reveals evidence for a large nosocomial outbreak in Belgium

scientific article published on 16 July 2009

Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methods.

scientific article published in November 2004

Phylogenetic relationships of the HA and NA genes between vaccine and seasonal influenza A(H3N2) strains in Korea

scientific article

Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A.

scientific article published on 21 December 2011

Phylogeography and population dynamics of dengue viruses in the Americas

scientific article

Phylogeography of dengue virus serotype 4, Brazil, 2010-2011.

scientific article published on November 2012

Phylogeography takes a relaxed random walk in continuous space and time

scientific article

Plasma exchange-associated immunoglobulin m-negative hantavirus disease after a camping holiday in southern france

scientific article published on 26 April 2004

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

scientific article published on 7 January 2016

Rates of viral evolution are linked to host geography in bat rabies

scientific article

Reassortment compatibility between PB1, PB2, and HA genes of the two influenza B virus lineages in mammalian cells

scientific article published on 08 June 2016

Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form

scientific article

Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa

scientific article

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

scientific article

Reconstruction of the origin and dispersal of the worldwide dominant Hepatitis B Virus subgenotype D1

scientific article published in 2022

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

scientific article

Role of viral evolutionary rate in HIV-1 disease progression in a linked cohort

scientific article

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

scientific article

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

scientific article

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

scientific article

Single cell analysis of lymph node tissue from HIV-1 infected patients reveals that the majority of CD4+ T-cells contain one HIV-1 DNA molecule

scientific article

Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals

scientific article published in 2022

Spatial dynamics of human-origin H1 influenza A virus in North American swine

scientific article

Synonymous and nonsynonymous distances help untangle convergent evolution and recombination

scientific article published in August 2015

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics

scientific article

Temporal signal and the phylodynamic threshold of SARS-CoV-2

scientific article published on 01 July 2020

The International Virus Bioinformatics Meeting 2022

publication published on 05 May 2022

The Spread of Tomato Yellow Leaf Curl Virus from the Middle East to the World ⬇️

scientific article published on October 28, 2010

The comparative genomics of human respiratory syncytial virus subgroups A and B: genetic variability and molecular evolutionary dynamics

scientific article published on 22 May 2013

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

scientific article

The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates

scientific article (publication date: April 2014)

The mode and tempo of hepatitis C virus evolution within and among hosts ⬇️

scientific article

The molecular population genetics of HIV-1 group O

scientific article

The phylogeography and spatiotemporal spread of south-central skunk rabies virus

scientific article

The recent ancestry of Middle East respiratory syndrome coronavirus in Korea has been shaped by recombination

scientific article

Three roads diverged? Routes to phylogeographic inference ⬇️

scientific article published on September 20, 2010

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

scientific article

Toward a quantitative understanding of viral phylogeography

scientific article published on 28 October 2011

Towards a unified classification for human respiratory syncytial virus genotypes

scientific article published on 24 July 2020

Tracing the origin and history of the HIV-2 epidemic

scientific article

U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains

scientific article

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

scientific article

Unifying the spatial epidemiology and molecular evolution of emerging epidemics

scientific article

Unlocking capacities of genomics for the COVID-19 response and future pandemics

scientific article published on 08 April 2022

Untangling introductions and persistence in COVID-19 resurgence in Europe

scholarly article by Philippe Lemey published in 2021

Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages - Application to rabies virus spread in Iran

scientific article published on 18 September 2019

Virus evolution and transmission in an ever more connected world

scientific article

Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains

article

Yellow fever virus maintenance in Trinidad and its dispersal throughout the Americas

scientific article

nosoi: A stochastic agent-based transmission chain simulation framework in r

scientific article published on 21 June 2020

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

scientific article

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