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Philippe Lemey

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Belgium

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TOP 3
Makiko Kondo; Philippe Lemey; Tetsuro Matano; Hiroko Sagara; Takako Sano; Natsuo Tachikawa; Mitsunobu Imai; Ichiro Itoda; Shinya Iwamuro; Shingo Kato; Ko Yamanaka; Yukihiro Yoshimura; Yutaka Takebe
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.
Gabriela B Cybis; Philippe Lemey; Janet S Sinsheimer; Marc A Suchard
Graph hierarchies for phylogeography.
Nuno Rodrigues Faria; Andrew Rambaut; Daniel G Streicker; Marc A Suchard; Philippe Lemey
Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints.

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All Publications

2013: Makiko Kondo; Philippe Lemey; Tetsuro Matano; Hiroko Sagara; Takako Sano; Natsuo Tachikawa; Mitsunobu Imai; Ichiro Itoda; Shinya Iwamuro; Shingo Kato; Ko Yamanaka; Yukihiro Yoshimura; Yutaka Takebe
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.
Journal of virology 2013;87(10):5351-61.
2013: Gabriela B Cybis; Philippe Lemey; Janet S Sinsheimer; Marc A Suchard
Graph hierarchies for phylogeography.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368(1614):20120206.
2013: Nuno Rodrigues Faria; Andrew Rambaut; Daniel G Streicker; Marc A Suchard; Philippe Lemey
Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368(1614):20120196.
2013: Mandev S Gill; Philippe Lemey; Andrew Rambaut; Beth Shapiro; Nuno R Faria; Marc A Suchard
Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci.
Molecular biology and evolution 2013;30(3):713-24.
2013: Guy Baele; Alexei J Drummond; Wai Lok Sibon Li; Marc A Suchard; Philippe Lemey
Accurate model selection of relaxed molecular clocks in bayesian phylogenetics.
Molecular biology and evolution 2013;30(2):239-43.
2013: Cintia Bittar; Claudia Márcia Aparecida Carareto; Isabel Maria Vicente Guedes de Carvalho-Mello; Ana Carolina Gomes Jardim; Philippe Lemey; J R R Pinho; Lilian Hiromi Tomonari Yamasaki; Paula Rahal
On Hepatitis C Virus Evolution: The Interaction between Virus and Host towards Treatment Outcome.
PloS one 2013;8(4):e62393.
2013: Lieselot Houspie; Els Keyaerts; Philippe Lemey; Eva Reijmen; Freya Vaeyens; Anne Vankeerberghen; Valentijn Vergote; Hans De Beenhouwer; Marc Van Ranst
Circulation of HRSV in Belgium: From Multiple Genotype Circulation to Prolonged Circulation of Predominant Genotypes.
PloS one 2013;8(4):e60416.
2013: Guy Baele; Philippe Lemey; Stijn Vansteelandt
Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution.
BMC bioinformatics 2013;14():85.
2012: 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.
Bioinformatics (Oxford, England) 2012;28(24):3248-56.
2012: Marcio Roberto Teixeira Nunes; Eliana Vieira Pinto da Silva; Sueli Guerreiro Rodrigues; Clayton Pereira Silva de Lima; Edivaldo Costa Sousa; Marc A Suchard; Helena Baldez Vasconcelos; Ana Abecasis; Jedson Ferreira Cardoso; Valéria Lima Carvalho; Nuno Rodrigues Faria; Philippe Lemey; Daniele Barbosa de Almeida Medeiros; Keley Nascimento Barbosa Nunes; Pedro Fernando da Costa Vasconcelos
Phylogeography of dengue virus serotype 4, Brazil, 2010-2011.
Emerging infectious diseases 2012;18(11):1858-64.
2012: Lucy A Weinert; John J Welch; Philippe Lemey; Andrew Rambaut; Marc A Suchard; J Ross Fitzgerald
Molecular dating of human-to-bovid host jumps by Staphylococcus aureus reveals an association with the spread of domestication.
Biology letters 2012;8(5):829-32.
2012: Oliver G Pybus; Andrew Rambaut; Susan L Stramer; Marc A Suchard; Nimalan Arinaminpathy; Flavien J Bernardin; Michael P Busch; Forrest W Crawford; Rebecca R Gray; Philippe Lemey; Eric L Delwart
Unifying the spatial epidemiology and molecular evolution of emerging epidemics.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(37):15066-71.
2012: Guy Baele; Trevor Bedford; Philippe Lemey; Andrew Rambaut; Marc A Suchard; Alexander V Alekseyenko
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty.
Molecular biology and evolution 2012;29(9):2157-67.
2012: Remco Bouckaert; Alexei J Drummond; Michael Dunn; Russell D Gray; Simon J Greenhill; Philippe Lemey; Marc A Suchard; Alexander V Alekseyenko; Quentin D Atkinson
Mapping the origins and expansion of the Indo-European language family.
Science (New York, N.Y.) 2012;337(6097):957-60.
2012: Tommy Tsan-Yuk Lam; Philippe Lemey; Edward C Holmes; Chung Chau Hon; Jingwei Jiang; Jun Li; Oliver G Pybus; Mang Shi; Hein Min Tun; Frederick Chi-Ching Leung
Phylodynamics of H5N1 avian influenza virus in Indonesia.
Molecular ecology 2012;21(12):3062-77.
2012: Orchid M Allicock; Shannon N Bennett; Jerome E Foster; Philippe Lemey; Brandi A Mueller; Oliver G Pybus; Andrew Rambaut; Marc A Suchard; Andrew Tatem; Christine Carrington
Phylogeography and population dynamics of dengue viruses in the Americas.
Molecular biology and evolution 2012;29(6):1533-43.
2012: Nuno R Faria; Maria F Gonçalves; Patrick Goubau; Ioannis Hodges-Mameletzis; Sabelle Jallow; Ricardo Camacho; João D de Sousa; Smit Erasmus; Stefania Paolucci; Danuta Pieniazek; Berta Rodés; Jean Ruelle; Joana C Silva; Vincent Soriano; Marc A Suchard; Nuno Taveira; Ana Treviño; Anne-Mieke Vandamme; Li Xu; Philippe Lemey
Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A.
The Journal of general virology 2012;93(Pt 4):889-99.
2012: Nuno R Faria; Ana Abecasis; Idalina Bonfim; Ricardo Camacho; Nicaise Ndembi; João D Sousa; Marc A Suchard; Anne-Mieke Vandamme; Philippe Lemey
Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2012;12(2):453-60.
2012: Diana Edo-Matas; Philippe Lemey; Andrea Rachinger; Laurentia C Setiawan; Angélique B van 't Wout; Brigitte D Boeser-Nunnink; Hanneke Schuitemaker
The evolution of human immunodeficiency virus type-1 (HIV-1) envelope molecular properties and coreceptor use at all stages of infection in an HIV-1 donor-recipient pair.
Virology 2012;422(1):70-80.
2012: Lydia Tan; Grada M van Bleek; Anton M van Loon; Emmanuel J H J Wiertz; Marco C Viveen; Lieselot Houspie; Nicolaas J G Jansen; Philippe Lemey; Darren P Martin; Frank E J Coenjaerts
Genetic variability among complete human respiratory syncytial virus subgroup A genomes: bridging molecular evolutionary dynamics and epidemiology.
PloS one 2012;7(12):e51439.
2012: Daniel G Streicker; Andres Velasco-Villa; Philippe Lemey; Charles E Rupprecht
Rates of viral evolution are linked to host geography in bat rabies.
PLoS pathogens 2012;8(5):e1002720.
2011: Nuno Rodrigues Faria; Andrew Rambaut; Marc A Suchard; Philippe Lemey
Toward a quantitative understanding of viral phylogeography.
Current opinion in virology 2011;1(5):423-9.
2011: Mahmoud Reza Pourkarim; Mustafizur Rahman; Eric Vanwijngaerden; Jannick Verbeeck; Samad Amini-Bavil-Olyaee; Lieselot Houspie; Philippe Lemey; Piet Maes; Frederik Nevens; Marc Van Ranst
Molecular characterization of hepatitis B virus strains circulating in Belgian patients co-infected with HIV and HBV: overt and occult infection.
Journal of medical virology 2011;83(11):1876-84.
2011: Darren P Martin; Philippe Lemey; David Posada
Analysing recombination in nucleotide sequences.
Molecular ecology resources 2011;11(6):943-55.
2011: Filip Bielejec; Andrew Rambaut; Marc A Suchard; Philippe Lemey
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics.
Bioinformatics (Oxford, England) 2011;27(20):2910-2.
2011: Adérito L Monjane; Sunday Oluwafemi; Betty E Owor; Moses Ramusi; Edward Rybicki; Silla Semballa; Dionne Shepherd; Michelo Simuyandi; Rizwan Syed; Appolinaire Tagne; Fidèle Tiendrébéogo; Tania van Antwerpen; Rob W Briddon; Julia B Erdmann; Bradley Flett; Gordon W Harkins; Ephrem K Komba; Didier P Lakoutene; Pierre Lefeuvre; Philippe Lemey; Jean-Michel Lett; Noella Mandakombo; Peter G Markham; Darren Martin; Joseph Mboukoulida; Oliver P Windram; Innocent Zinga; Arvind Varsani
Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa.
Journal of virology 2011;85(18):9623-36.
2011: Ceiridwen J Edwards; Tara L Fulton; Philippe Lemey; Eline D Lorenzen; Nigel Monaghan; Tamsin C O'Connell; Andrew Rambaut; Ian Barnes; Ross Barnett; Gennady F Baryshnikov; Daniel G Bradley; Peter Coxon; Marc A Suchard; Mark Thomas; Cristina Valdiosera; John J Welch; Eske Willerslev; Beth Shapiro
Ancient hybridization and an Irish origin for the modern polar bear matriline.
Current biology : CB 2011;21(15):1251-8.
2011: Nicaise Ndembi; Charlotte Ngansop; Alash'Le Abimiku; Shizuka Iwamoto; Lazare Kaptue; Philippe Lemey; Dora Mbanya; Eiji Ido
High frequency of HIV-1 dual infections in Cameroon, West Central Africa.
Journal of acquired immune deficiency syndromes (1999) 2011;57(2):e25-7.
2011: Martha I Nelson; Andrew Rambaut; Marc A Suchard; Yi Tan; Cécile Viboud; Amy Vincent; Susan Detmer; Edward C Holmes; Tommy Tsan-Yuk Lam; Philippe Lemey; Marie Gramer
Spatial dynamics of human-origin H1 influenza A virus in North American swine.
PLoS pathogens 2011;7(6):e1002077.
2011: M R Pourkarim; Samad Amini-Bavil-Olyaee; Philippe Lemey; P Maes; Marc Van Ranst
HBV subgenotype misclassification expands quasi-subgenotype A3.
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 2011;17(6):947-9.
2011: Andrea Rachinger; Paul H P Groeneveld; Philippe Lemey; Sander van Assen; Hanneke Schuitemaker
Time-measured phylogenies of gag, pol and env sequence data reveal the direction and time interval of HIV-1 transmission.
AIDS (London, England) 2011;25(8):1035-9.
2011: Diana Edo-Matas; Philippe Lemey; Jennifer A Tom; Cèlia Serna-Bolea; Agnes E van den Blink; Angélique B van 't Wout; Hanneke Schuitemaker; Marc A Suchard
Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models.
Molecular biology and evolution 2011;28(5):1605-16.
2011: Andrea Schulze; Philippe Lemey; Jörg Schubert; Myra O McClure; Axel Rethwilm; Jochen Bodem
Complete nucleotide sequence and evolutionary analysis of a gorilla foamy virus.
The Journal of general virology 2011;92(Pt 3):582-6.
2011: Abby Harrison; Susanne Horn; Matthew Hurles; Philippe Lemey; Joji Malani; Andrew Masta; Chris Moyes; David Penny; Jan Pryor; Andrew Rambaut; Mathias Supuri; Burentau Teriboriki; Tebuka Toatu; Beth Shapiro
Genomic analysis of hepatitis B virus reveals antigen state and genotype as sources of evolutionary rate variation.
Viruses 2011;3(2):83-101.
2011: Carita Savolainen-Kopra; Anja Paananen; Soile Blomqvist; Päivi Klemola; Marja-Leena Simonen; Maija Lappalainen; Tytti Vuorinen; Markku Kuusi; Philippe Lemey; Merja Roivainen
A large Finnish echovirus 30 outbreak was preceded by silent circulation of the same genotype.
Virus genes 2011;42(1):28-36.
2011: Rebecca R Gray; Aris Katzourakis; Philippe Lemey; Joe Parker; Marco Salemi; Oliver G Pybus
The mode and tempo of hepatitis C virus evolution within and among hosts.
BMC evolutionary biology 2011;11():131.
2010: Erik W Bloomquist; Philippe Lemey; Marc A Suchard
Three roads diverged? Routes to phylogeographic inference.
Trends in ecology & evolution 2010;25(11):626-32.
2010: Jannick Verbeeck; L Kwanten; Francois D'heygere; A Beguin; Stefan Michiels; I Desombere; Geert Leroux-Roels; Philippe Lemey; Frederik Nevens; Marc Van Ranst
HCV genotype distribution in Flanders and Brussels (Belgium): unravelling the spread of an uncommon HCV genotype 5a cluster.
European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology 2010;29(11):1427-34.
2010: Darren P Martin; Philippe Lemey; Martin Lott; Vincent Moulton; David Posada; Pierre Lefeuvre
RDP3: a flexible and fast computer program for analyzing recombination.
Bioinformatics (Oxford, England) 2010;26(19):2462-3.
2010: Maria Gullberg; Conny Tolf; Nina Jonsson; Mick N Mulders; Carita Savolainen-Kopra; Tapani Hovi; Marc Van Ranst; Philippe Lemey; Susan Hafenstein; A Michael Lindberg
Characterization of a putative ancestor of coxsackievirus B5.
Journal of virology 2010;84(19):9695-708.
2010: Albert J Auguste; Philippe Lemey; Oliver G Pybus; Marc A Suchard; Rosa Alba Salas; Abiodun A Adesiyun; Alan D Barrett; Robert B Tesh; Scott C Weaver; Christine Carrington
Yellow fever virus maintenance in Trinidad and its dispersal throughout the Americas.
Journal of virology 2010;84(19):9967-77.
2010: Jelle Matthijnssens; Elisabeth Heylen; Mark Zeller; Mustafizur Rahman; Philippe Lemey; Marc Van Ranst
Phylodynamic analyses of rotavirus genotypes G9 and G12 underscore their potential for swift global spread.
Molecular biology and evolution 2010;27(10):2431-6.
2010: Sabine van der Sanden; Harrie van Der Avoort; Philippe Lemey; Gökhan Uslu; Marion Koopmans
Evolutionary trajectory of the VP1 gene of human enterovirus 71 genogroup B and C viruses.
The Journal of general virology 2010;91(Pt 8):1949-58.
2010: Philippe Lemey; Andrew Rambaut; John J Welch; Marc A Suchard
Phylogeography takes a relaxed random walk in continuous space and time.
Molecular biology and evolution 2010;27(8):1877-85.
2010: J Joukje Siebenga; Philippe Lemey; Sergei L Kosakovsky Pond; Andrew Rambaut; Harry Vennema; Marion Koopmans
Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants.
PLoS pathogens 2010;6(5):e1000884.
2010: Bram Vrancken; Sébastian Lequime; Kristof Theys; Philippe Lemey
Covering all bases in HIV research: unveiling a hidden world of viral evolution.
AIDS reviews 2010;12(2):89-102.
2010: Mahmoud Reza Pourkarim; Samad Amini-Bavil-Olyaee; Philippe Lemey; Piet Maes; Marc Van Ranst
Are hepatitis B virus "subgenotypes" defined accurately?
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2010;47(4):356-60.
2010: Paula F Campos; Eske Willerslev; Andrei Sher; Ludovic Orlando; Erik Axelsson; Alexei Tikhonov; Kim Aaris-Sørensen; Alex D Greenwood; Ralf-Dietrich Kahlke; Pavel Kosintsev; Tatiana Krakhmalnaya; Tatyana Kuznetsova; Philippe Lemey; Ross D E MacPhee; Christopher A Norris; Kieran Shepherd; Marc A Suchard; Grant D Zazula; Beth Shapiro; M Thomas P Gilbert
Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(12):5675-80.
2010: Mahmoud Reza Pourkarim; Samad Amini-Bavil-Olyaee; Jannick Verbeeck; Philippe Lemey; Mark Zeller; Mustafizur Rahman; Piet Maes; Frederik Nevens; Marc Van Ranst
Molecular evolutionary analysis and mutational pattern of full-length genomes of hepatitis B virus isolated from Belgian patients with different clinical manifestations.
Journal of medical virology 2010;82(3):379-89.
2010: Chiraz Talbi; Philippe Lemey; Marc A Suchard; Elbia Abdelatif; Mehdi Elharrak; Jalal Nourlil; Nourlil Jalal; Abdellah Faouzi; Juan E Echevarría; Sonia Vazquez Morón; Andrew Rambaut; Nicholas Campiz; Andrew J Tatem; Edward C Holmes; Hervé Bourhy
Phylodynamics and human-mediated dispersal of a zoonotic virus.
PLoS pathogens 2010;6(10):e1001166.
2010: Pierre Lefeuvre; Darren Martin; Gordon Harkins; Philippe Lemey; Alistair J A Gray; Sandra Meredith; Francisco Lakay; Adérito Monjane; Jean-Michel Lett; Arvind Varsani; Jahangir Heydarnejad
The spread of tomato yellow leaf curl virus from the Middle East to the world.
PLoS pathogens 2010;6(10):e1001164.
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 bioinformatics 2010;11():409.
2010: João Dinis de Sousa; Viktor Müller; Philippe Lemey; Anne-Mieke Vandamme
High GUD incidence in the early 20 century created a particularly permissive time window for the origin and initial spread of epidemic HIV strains.
PloS one 2010;5(4):e9936.
2010: Mahmoud Reza Pourkarim; Philippe Lemey; Samad Amini-Bavil-Olyaee; Piet Maes; Marc Van Ranst
Novel hepatitis B virus subgenotype A6 in African-Belgian patients.
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2010;47(1):93-6.
2009: Ana B Abecasis; Anne-Mieke Vandamme; Philippe Lemey
Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution.
Journal of virology 2009;83(24):12917-24.
2009: Sarah M McDonald; Jelle Matthijnssens; John K McAllen; Erin Hine; Larry Overton; Shiliang Wang; Philippe Lemey; Mark Zeller; Marc Van Ranst; David J Spiro; John T Patton
Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.
PLoS pathogens 2009;5(10):e1000634.
2009: For Yue Tso; Federico Guillermo Hoffmann; Damien Tully; Philippe Lemey; Robert A Rasmussen; Hong Zhang; Ruth Ruprecht; Charles Wood
A comparative study of HIV-1 clade C env evolution in a Zambian infant with an infected rhesus macaque during disease progression.
AIDS (London, England) 2009;23(14):1817-28.
2009: Philippe Lemey; Andrew Rambaut; Alexei J Drummond; Marc A Suchard
Bayesian phylogeography finds its roots.
PLoS computational biology 2009;5(9):e1000520.
2009: Mahmoud Reza Pourkarim; Jannick Verbeeck; Mustafizur Rahman; Samad Amini-Bavil-Olyaee; An-Marie Forier; Philippe Lemey; Piet Maes; Marc Van Ranst
Phylogenetic analysis of hepatitis B virus full-length genomes reveals evidence for a large nosocomial outbreak in Belgium.
Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2009;46(1):61-8.
2009: Philippe Lemey; Marc Suchard; Andrew Rambaut
Reconstructing the initial global spread of a human influenza pandemic: A Bayesian spatial-temporal model for the global spread of H1N1pdm.
PLoS currents 2009;1():RRN1031.
2009: Philippe Lemey; Martin Lott; Darren P Martin; Vincent Moulton
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning.
BMC bioinformatics 2009;10():126.
2009: Elizabeth S Machado; Adriana O Afonso; Dwight V Nissley; Philippe Lemey; Silvia M Cunha; Ricardo H Oliveira; Marcelo A Soares
Emergence of primary NNRTI resistance mutations without antiretroviral selective pressure in a HAART-treated child.
PloS one 2009;4(3):e4806.
2009: Filippo Canducci; Maria Chiara Marinozzi; Michela Sampaolo; Stefano Berrè; Patrizia Bagnarelli; Massimo Degano; Giulia Gallotta; Benedetta Mazzi; Philippe Lemey; Roberto Burioni; Massimo Clementi
Dynamic features of the selective pressure on the human immunodeficiency virus type 1 (HIV-1) gp120 CD4-binding site in a group of long term non progressor (LTNP) subjects.
Retrovirology 2009;6():4.
2009: Oliver G Pybus; Eleanor Barnes; Rachel Taggart; Philippe Lemey; Peter V Markov; Bouachan Rasachak; Bounkong Syhavong; Rattanaphone Phetsouvanah; Isabelle Sheridan; Isla S Humphreys; Ling Lu; Paul N Newton; Paul Klenerman
Genetic history of hepatitis C virus in East Asia.
Journal of virology 2009;83(2):1071-82.
2008: Annabel Rector; Hans Stevens; Géraldine Lacave; Philippe Lemey; Sara Mostmans; Ana Salbany; Melissa Vos; Koenraad Van Doorslaer; Shin-Je Ghim; Manuela Rehtanz; Gregory D Bossart; A Bennett Jenson; Marc Van Ranst
Genomic characterization of novel dolphin papillomaviruses provides indications for recombination within the Papillomaviridae.
Virology 2008;378(1):151-61.
2008: Catharina Matheï; Sonia Van Dooren; Philippe Lemey; Pierre Van Damme; Frank Buntinx; Anne-Mieke Vandamme
The epidemic history of hepatitis C among injecting drug users in Flanders, Belgium.
Journal of viral hepatitis 2008;15(6):399-408.
2008: Federico Guillermo Hoffmann; Xiang He; John T West; Philippe Lemey; Chipepo Kankasa; Charles Wood
Genetic variation in mother-child acute seroconverter pairs from Zambia.
AIDS (London, England) 2008;22(7):817-24.
2008: 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.
Bioinformatics (Oxford, England) 2008;24(1):34-41.
2007: 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.
Journal of computational biology : a journal of computational molecular cell biology 2007;14(8):1105-14.
2007: Ana Abecasis; Philippe Lemey; Nicole Vidal; Tulio De Oliveira; Martine Peeters; Ricardo Camacho; Beth Shapiro; Andrew Rambaut; Anne-Mieke Vandamme
Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form.
Journal of virology 2007;81(16):8543-51.
2007: Sonia Resik; Philippe Lemey; Li-Hua Ping; Vivian Kouri; Jose Joanes; Jorge Pérez; Anne-Mieke Vandamme; Ronald Swanstrom
Limitations to contact tracing and phylogenetic analysis in establishing HIV type 1 transmission networks in Cuba.
AIDS research and human retroviruses 2007;23(3):347-56.
2007: 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 computational biology 2007;3(2):e29.
2007: Annabel Rector; Philippe Lemey; Ruth Tachezy; Sara Mostmans; Shin-Je Ghim; Koenraad Van Doorslaer; Melody E Roelke-Parker; R BUSH; RICHARD MONTALI; Janis Joslin; Robert D Burk; A Bennett Jenson; John P Sundberg; Beth Shapiro; Marc Van Ranst
Ancient papillomavirus-host co-speciation in Felidae.
Genome biology 2007;8(4):R57.
2006: Philippe Lemey; Andrew Rambaut; Oliver G Pybus
HIV evolutionary dynamics within and among hosts.
AIDS reviews 2006;8(3):125-40.
2006: Leen Vijgen; Els Keyaerts; Philippe Lemey; Piet Maes; Kristien Van Reeth; Hans Nauwynck; Maurice B Pensaert; Marc Van Ranst
Evolutionary history of the closely related group 2 coronaviruses: porcine hemagglutinating encephalomyelitis virus, bovine coronavirus, and human coronavirus OC43.
Journal of virology 2006;80(14):7270-4.
2006: Jannick Verbeeck; Piet Maes; Philippe Lemey; Oliver G Pybus; Elke Wollants; Ernie Song; Frederik Nevens; Johan Fevery; Wayne Delport; Schalk W van der Merwe; Marc Van Ranst
Investigating the origin and spread of hepatitis C virus genotype 5a.
Journal of virology 2006;80(9):4220-6.
2006: Simon J Potter; Philippe Lemey; Wayne B Dyer; John Sullivan; Choo Beng Chew; Anne-Mieke Vandamme; Dominic E Dwyer; Nitin K Saksena
Genetic analyses reveal structured HIV-1 populations in serially sampled T lymphocytes of patients receiving HAART.
Virology 2006;348(1):35-46.
2005: Philippe Lemey; Sonia Van Dooren; Kristel Van Laethem; Yoeri Schrooten; Inge Derdelinckx; Patrick Goubau; Françoise Brun-Vézinet; Dolores Vaira; Anne-Mieke Vandamme
Molecular testing of multiple HIV-1 transmissions in a criminal case.
AIDS (London, England) 2005;19(15):1649-58.
2005: Philippe Lemey; Anne-Mieke Vandamme
Exploring full-genome sequences for phylogenetic support of HIV-1 transmission events.
AIDS (London, England) 2005;19(14):1551-2.
2005: Philippe Lemey; Inge Derdelinckx; Andrew Rambaut; Kristel Van Laethem; Stephanie Dumont; Steve Vermeulen; Eric Van Wijngaerden; Anne-Mieke Vandamme
Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain.
Journal of virology 2005;79(18):11981-9.
2005: Kalina T Zlateva; Philippe Lemey; Elien Moës; Anne-Mieke Vandamme; Marc Van Ranst
Genetic variability and molecular evolution of the human respiratory syncytial virus subgroup B attachment G protein.
Journal of virology 2005;79(14):9157-67.
2005: Annabel Rector; Koenraad Van Doorslaer; Mads Frost Bertelsen; Ian Barker; Rolf-Arne Olberg; Philippe Lemey; John P Sundberg; Marc Van Ranst
Isolation and cloning of the raccoon (Procyon lotor) papillomavirus type 1 by using degenerate papillomavirus-specific primers.
The Journal of general virology 2005;86(Pt 7):2029-33.
2005: Sonia Van Dooren; Laurent Meertens; Philippe Lemey; Antoine Gessain; Anne-Mieke Vandamme
Full-genome analysis of a highly divergent simian T-cell lymphotropic virus type 1 strain in Macaca arctoides.
The Journal of general virology 2005;86(Pt 7):1953-9.
2005: Leen Vijgen; Els Keyaerts; Philippe Lemey; Elien Moës; Sandra Li; Anne-Mieke Vandamme; Marc Van Ranst
Circulation of genetically distinct contemporary human coronavirus OC43 strains.
Virology 2005;337(1):85-92.
2005: Meriet Mikhail; Bin Wang; Philippe Lemey; Brenda Beckholdt; Anne-Mieke Vandamme; Michael John Gill; Nitin K Saksena
Full-length HIV type 1 genome analysis showing evidence for HIV type 1 transmission from a nonprogressor to two recipients who progressed to AIDS.
AIDS research and human retroviruses 2005;21(6):575-9.
2005: Philippe Lemey; Oliver G Pybus; Sonia Van Dooren; Anne-Mieke Vandamme
A Bayesian statistical analysis of human T-cell lymphotropic virus evolutionary rates.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2005;5(3):291-8.
2005: Philippe Lemey; Sonia Van Dooren; Anne-Mieke Vandamme
Evolutionary dynamics of human retroviruses investigated through full-genome scanning.
Molecular biology and evolution 2005;22(4):942-51.
2005: Dimitrios Paraskevis; Koen Deforche; Philippe Lemey; Gkikas Magiorkinis; A Hatzakis; Anne-Mieke Vandamme
SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference.
Bioinformatics (Oxford, England) 2005;21(7):1274-5.
2005: Leen Vijgen; Philippe Lemey; Els Keyaerts; Marc Van Ranst
Genetic variability of human respiratory coronavirus OC43.
Journal of virology 2005;79(5):3223-4; author reply 3224-5.
2005: Leen Vijgen; Els Keyaerts; Elien Moës; Inge Thoelen; Elke Wollants; Philippe Lemey; Anne-Mieke Vandamme; Marc Van Ranst
Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event.
Journal of virology 2005;79(3):1595-604.
2005: Meriet Mikhail; Bin Wang; Philippe Lemey; Brenda Beckthold; Anne-Mieke Vandamme; Michael John Gill; Nitin K Saksena
Role of viral evolutionary rate in HIV-1 disease progression in a linked cohort.
Retrovirology 2005;2():41.
2005: Kristel Van Laethem; Yoeri Schrooten; Philippe Lemey; Eric Van Wijngaerden; Stéphane De Wit; Marc Van Ranst; Anne-Mieke Vandamme
A genotypic resistance assay for the detection of drug resistance in the human immunodeficiency virus type 1 envelope gene.
Journal of virological methods 2005;123(1):25-34.
2004: Korneel Hens; Philippe Lemey; Nathalie Macours; Carmen Francis; Roger Huybrechts
Cyclorraphan yolk proteins and lepidopteran minor yolk proteins originate from two unrelated lipase families.
Insect molecular biology 2004;13(6):615-23.
2004: Dimitrios Paraskevis; Emmanouil Magiorkinis; Gkikas Magiorkinis; Vassilios G Kiosses; Philippe Lemey; Anne-Mieke Vandamme; Andrew Rambaut; Angelos Hatzakis
Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methods.
Journal of molecular evolution 2004;59(5):709-17.
2004: Simon J Potter; Philippe Lemey; Guillaume Achaz; Choo Beng Chew; Anne-Mieke Vandamme; Dominic E Dwyer; Nitin K Saksena
HIV-1 compartmentalization in diverse leukocyte populations during antiretroviral therapy.
Journal of leukocyte biology 2004;76(3):562-70.
2004: Philippe Lemey; Oliver G Pybus; Andrew Rambaut; Alexei J Drummond; David L Robertson; Pierre Roques; Michael Worobey; Anne-Mieke Vandamme
The molecular population genetics of HIV-1 group O.
Genetics 2004;167(3):1059-68.
2004: Els Keyaerts; Erik Ghijsels; Philippe Lemey; Piet Maes; Pierre Zachée; Ronny Daelemans; Tony Vervoort; Gerhard Mertens; Marc Van Ranst; Jan Clement
Plasma exchange-associated immunoglobulin m-negative hantavirus disease after a camping holiday in southern france.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2004;38(10):1350-6.
2004: Kalina T Zlateva; Philippe Lemey; Anne-Mieke Vandamme; Marc Van Ranst
Molecular evolution and circulation patterns of human respiratory syncytial virus subgroup a: positively selected sites in the attachment g glycoprotein.
Journal of virology 2004;78(9):4675-83.
2004: Inge Thoelen; Elien Moës; Philippe Lemey; Sara Mostmans; Elke Wollants; A Michael Lindberg; Anne-Mieke Vandamme; Marc Van Ranst
Analysis of the serotype and genotype correlation of VP1 and the 5' noncoding region in an epidemiological survey of the human enterovirus B species.
Journal of clinical microbiology 2004;42(3):963-71.
2003: Dimitrios Paraskevis; Philippe Lemey; Marco Salemi; M Suchard; Y Van De Peer; Anne-Mieke Vandamme
Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using bayesian inference: implications for the origin of HIV-1.
Molecular biology and evolution 2003;20(12):1986-96.
2003: Philippe Lemey; Marco Salemi; Bin Wang; Margaret Duffy; William H Hall; Nitin K Saksena; Anne-Mieke Vandamme
Site stripping based on likelihood ratio reduction is a useful tool to evaluate the impact of non-clock-like behavior on viral phylogenetic reconstructions.
FEMS immunology and medical microbiology 2003;39(2):125-32.
2003: Inge Thoelen; Philippe Lemey; Ingrid Van der Donck; Kurt Beuselinck; A Michael Lindberg; Marc Van Ranst
Molecular typing and epidemiology of enteroviruses identified from an outbreak of aseptic meningitis in Belgium during the summer of 2000.
Journal of medical virology 2003;70(3):420-9.
2003: Kenneth E Robbins; Philippe Lemey; Oliver G Pybus; Harold W Jaffe; Ae Youngpairoj; Teresa M Brown; Marco Salemi; Anne-Mieke Vandamme; Marcia L Kalish
U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains.
Journal of virology 2003;77(11):6359-66.
2003: Philippe Lemey; Oliver G Pybus; Bin Wang; Nitin K Saksena; Marco Salemi; Anne-Mieke Vandamme
Tracing the origin and history of the HIV-2 epidemic.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(11):6588-92.
2002: Nathalie Charlier; Pieter Leyssen; Cornelis W A Pleij; Philippe Lemey; Frédérique Billoir; Kristel Van Laethem; Anne-Mieke Vandamme; Erik De Clercq; Xavier de Lamballerie; Johan Neyts
Complete genome sequence of Montana Myotis leukoencephalitis virus, phylogenetic analysis and comparative study of the 3' untranslated region of flaviviruses with no known vector.
The Journal of general virology 2002;83(Pt 8):1875-85.
2002: Philippe Lemey; Marco Salemi; Leda Bassit; Anne-Mieke Vandamme
Phylogenetic classification of TT virus groups based on the N22 region is unreliable.
Virus research 2002;85(1):47-59.
2002: Pieter Leyssen; Nathalie Charlier; Philippe Lemey; Frédérique Billoir; Anne-Mieke Vandamme; Erik De Clercq; Xavier de Lamballerie; Johan Neyts
Complete genome sequence, taxonomic assignment, and comparative analysis of the untranslated regions of the Modoc virus, a flavivirus with no known vector.
Virology 2002;293(1):125-40.
2001: Annabel Rector; Philippe Lemey; W Laffut; Els Keyaerts; Frank Struyf; Elke Wollants; S Vermeire; P Rutgeerts; Marc Van Ranst
Mannan-binding lectin (MBL) gene polymorphisms in ulcerative colitis and Crohn's disease.
Genes and immunity 2001;2(6):323-8.