Publications:
A selected list of publications:
Faria Nuno R, Rambaut Andrew, Suchard Marc A, Baele Guy, Bedford Trevor, Ward Melissa J, Tatem Andrew J, Sousa João D, Arinaminpathy Nimalan, Pépin Jacques, Posada David, Peeters Martine, Pybus Oliver G, Lemey Philippe
HIV epidemiology. The early spread and epidemic ignition of HIV-1 in
human populations
Science (New York, N.Y.),
2014; 346(6205):
56-61.
Strickland Samantha L, Rife Brittany D, Lamers Susanna L, Nolan David J, Veras Nazle M C, Prosperi Mattia C F, Burdo Tricia H, Autissier Patrick, Nowlin Brian, Goodenow Maureen M, Suchard Marc A, Williams Kenneth C, Salemi Marco
Spatiotemporal Dynamics of SIV Brain Infection in CD8+
Lymphocyte-Depleted Rhesus Macaques with NeuroAIDS
The Journal of general virology,
2014; 346(6205):
.
Jombart Thibaut, Aanensen David M, Baguelin Marc, Birrell Paul, Cauchemez Simon, Camacho Anton, Colijn Caroline, Collins Caitlin, Cori Anne, Didelot Xavier, Fraser Christophe, Frost Simon, Hens Niel, Hugues Joseph, Höhle Michael, Opatowski Lulla, Rambaut Andrew, Ratmann Oliver, Soubeyrand Samuel, Suchard Marc A, Wallinga Jacco, Ypma Rolf, Ferguson Neil
OutbreakTools: a new platform for disease outbreak analysis using the
R software
Epidemics,
2014; 7(4):
28-34.
Nunes Marcio R T, Palacios Gustavo, Faria Nuno Rodrigues, Sousa Edivaldo Costa, Pantoja Jamilla A, Rodrigues Sueli G, Carvalho Valéria L, Medeiros Daniele B A, Savji Nazir, Baele Guy, Suchard Marc A, Lemey Philippe, Vasconcelos Pedro F C, Lipkin W Ian
Air travel is associated with intracontinental spread of dengue virus
serotypes 1-3 in Brazil
PLoS neglected tropical diseases,
2014; 8(4):
e2769.
Vrancken Bram, Rambaut Andrew, Suchard Marc A, Drummond Alexei, Baele Guy, Derdelinckx Inge, Van Wijngaerden Eric, Vandamme Anne-Mieke, Van Laethem Kristel, Lemey Philippe
The genealogical population dynamics of HIV-1 in a large transmission
chain: bridging within and among host evolutionary rates
PLoS computational biology,
2014; 10(4):
e1003505.
Lemey Philippe, Rambaut Andrew, Bedford Trevor, Faria Nuno, Bielejec Filip, Baele Guy, Russell Colin A, Smith Derek J, Pybus Oliver G, Brockmann Dirk, Suchard Marc A
Unifying viral genetics and human transportation data to predict the
global transmission dynamics of human influenza H3N2
PLoS pathogens,
2014; 10(2):
e1003932.
Bedford Trevor, Suchard Marc A, Lemey Philippe, Dudas Gytis, Gregory Victoria, Hay Alan J, McCauley John W, Russell Colin A, Smith Derek J, Rambaut Andrew
Integrating influenza antigenic dynamics with molecular evolution
eLife,
2014; 3(1):
e01914.
Shi Mang, Lemey Philippe, Singh Brar Manreetpal, Suchard Marc A, Murtaugh Michael P, Carman Susy, D'Allaire Sylvie, Delisle Benjamin, Lambert Marie-Ãve, Gagnon Carl A, Ge Li, Qu Yihan, Yoo Dongwan, Holmes Edward C, Chi-Ching Leung Frederick
The spread of type 2 Porcine Reproductive and Respiratory Syndrome
Virus (PRRSV) in North America: a phylogeographic approach
Virology,
2013; 447(1-2):
146-54.
Cybis Gabriela B, Sinsheimer Janet S, Lemey Philippe, Suchard Marc A
Graph hierarchies for phylogeography
Philosophical transactions of the Royal Society of London. Series B, Biological sciences,
2013; 368(1614):
20120206.
Kemal Kimdar S, Ramirez Christina M, Burger Harold, Foley Brian, Mayers Douglas, Klimkait Thomas, Hamy François, Anastos Kathryn, Petrovic Katarina, Minin Vladimir N, Suchard Marc A, Weiser Barbara
Recombination between variants from genital tract and plasma:
evolution of multidrug-resistant HIV type 1
AIDS research and human retroviruses,
2012; 28(12):
1766-74.
Nunes Marcio Roberto Teixeira, Faria Nuno Rodrigues, Vasconcelos Helena Baldez, Medeiros Daniele Barbosa de Almeida, Silva de Lima Clayton Pereira, Carvalho Valéria Lima, Pinto da Silva Eliana Vieira, Cardoso Jedson Ferreira, Sousa Edivaldo Costa, Nunes Keley Nascimento Barbosa, Rodrigues Sueli Guerreiro, Abecasis Ana Barroso, Suchard Marc A, Lemey Philippe, Vasconcelos Pedro Fernando da Costa
Phylogeography of dengue virus serotype 4, Brazil, 2010-2011
Emerging infectious diseases,
2012; 18(11):
1858-64.
Pybus Oliver G, Suchard Marc A, Lemey Philippe, Bernardin Flavien J, Rambaut Andrew, Crawford Forrest W, Gray Rebecca R, Arinaminpathy Nimalan, Stramer Susan L, Busch Michael P, Delwart Eric L
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.
Bouckaert Remco, Lemey Philippe, Dunn Michael, Greenhill Simon J, Alekseyenko Alexander V, Drummond Alexei J, Gray Russell D, Suchard Marc A, Atkinson Quentin D
Mapping the origins and expansion of the Indo-European language
family
Science (New York, N.Y.),
2012; 337(6097):
957-60.
Allicock Orchid M, Lemey Philippe, Tatem Andrew J, Pybus Oliver G, Bennett Shannon N, Mueller Brandi A, Suchard Marc A, Foster Jerome E, Rambaut Andrew, Carrington Christine V F
Phylogeography and population dynamics of dengue viruses in the
Americas
Molecular biology and evolution,
2012; 29(6):
1533-43.
Ronquist Fredrik, Teslenko Maxim, van der Mark Paul, Ayres Daniel L, Darling Aaron, Höhna Sebastian, Larget Bret, Liu Liang, Suchard Marc A, Huelsenbeck John P
MrBayes 3.2: efficient Bayesian phylogenetic inference and model
choice across a large model space
Systematic biology,
2012; 61(3):
539-42.
Faria Nuno R, Hodges-Mameletzis Ioannis, Silva Joana C, Rodés Berta, Erasmus Smit, Paolucci Stefania, Ruelle Jean, Pieniazek Danuta, Taveira Nuno, Treviño Ana, Gonçalves Maria F, Jallow Sabelle, Xu Li, Camacho Ricardo J, Soriano Vincent, Goubau Patrick, de Sousa João D, Vandamme Anne-Mieke, Suchard Marc A, Lemey Philippe
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.
Faria Nuno R, Suchard Marc A, Abecasis Ana, Sousa João D, Ndembi Nicaise, Bonfim Idalina, Camacho Ricardo J, Vandamme Anne-Mieke, Lemey Philippe
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.
Ayres Daniel L, Darling Aaron, Zwickl Derrick J, Beerli Peter, Holder Mark T, Lewis Paul O, Huelsenbeck John P, Ronquist Fredrik, Swofford David L, Cummings Michael P, Rambaut Andrew, Suchard Marc A
BEAGLE: an application programming interface and high-performance
computing library for statistical phylogenetics
Systematic biology,
2012; 61(1):
170-3.
Lorenzen Eline D, Nogués-Bravo David, Orlando Ludovic, Weinstock Jaco, Binladen Jonas, Marske Katharine A, Ugan Andrew, Borregaard Michael K, Gilbert M Thomas P, Nielsen Rasmus, Ho Simon Y W, Goebel Ted, Graf Kelly E, Byers David, Stenderup Jesper T, Rasmussen Morten, Campos Paula F, Leonard Jennifer A, Koepfli Klaus-Peter, Froese Duane, Zazula Grant, Stafford Thomas W, Aaris-Sørensen Kim, Batra Persaram, Haywood Alan M, Singarayer Joy S, Valdes Paul J, Boeskorov Gennady, Burns James A, Davydov Sergey P, Haile James, Jenkins Dennis L, Kosintsev Pavel, Kuznetsova Tatyana, Lai Xulong, Martin Larry D, McDonald H Gregory, Mol Dick, Meldgaard Morten, Munch Kasper, Stephan Elisabeth, Sablin Mikhail, Sommer Robert S, Sipko Taras, Scott Eric, Suchard Marc A, Tikhonov Alexei, Willerslev Rane, Wayne Robert K, Cooper Alan, Hofreiter Michael, Sher Andrei, Shapiro Beth, Rahbek Carsten, Willerslev Eske
Species-specific responses of Late Quaternary megafauna to climate and
humans
Nature,
2011; 479(7373):
359-64.
Edwards Ceiridwen J, Suchard Marc A, Lemey Philippe, Welch John J, Barnes Ian, Fulton Tara L, Barnett Ross, O'Connell Tamsin C, Coxon Peter, Monaghan Nigel, Valdiosera Cristina E, Lorenzen Eline D, Willerslev Eske, Baryshnikov Gennady F, Rambaut Andrew, Thomas Mark G, Bradley Daniel G, Shapiro Beth
Ancient hybridization and an Irish origin for the modern polar bear
matriline
Current biology : CB,
2011; 21(15):
1251-8.
Nelson Martha I, Lemey Philippe, Tan Yi, Vincent Amy, Lam Tommy Tsan-Yuk, Detmer Susan, Viboud Cécile, Suchard Marc A, Rambaut Andrew, Holmes Edward C, Gramer Marie
Spatial dynamics of human-origin H1 influenza A virus in North
American swine
PLoS pathogens,
2011; 7(6):
e1002077.
Talbi Chiraz, Lemey Philippe, Suchard Marc A, Abdelatif Elbia, Elharrak Mehdi, Nourlil Jalal, Jalal Nourlil, Faouzi Abdellah, EchevarrÃa Juan E, Vazquez Morón Sonia, Rambaut Andrew, Campiz Nicholas, Tatem Andrew J, Holmes Edward C, Bourhy Hervé
Phylodynamics and human-mediated dispersal of a zoonotic virus
PLoS pathogens,
2010; 6(10):
e1001166.
Auguste Albert J, Lemey Philippe, Pybus Oliver G, Suchard Marc A, Salas Rosa Alba, Adesiyun Abiodun A, Barrett Alan D, Tesh Robert B, Weaver Scott C, Carrington Christine V F
Yellow fever virus maintenance in Trinidad and its dispersal
throughout the Americas
Journal of virology,
2010; 84(19):
9967-77.
Shi Binshan, Kitchen Christina, Weiser Barbara, Mayers Douglas, Foley Brian, Kemal Kimdar, Anastos Kathryn, Suchard Marc, Parker Monica, Brunner Cheryl, Burger Harold
Evolution and recombination of genes encoding HIV-1 drug resistance
and tropism during antiretroviral therapy
Virology,
2010; 404(1):
5-20.
Campos Paula F, Willerslev Eske, Sher Andrei, Orlando Ludovic, Axelsson Erik, Tikhonov Alexei, Aaris-Sørensen Kim, Greenwood Alex D, Kahlke Ralf-Dietrich, Kosintsev Pavel, Krakhmalnaya Tatiana, Kuznetsova Tatyana, Lemey Philippe, MacPhee Ross, Norris Christopher A, Shepherd Kieran, Suchard Marc A, Zazula Grant D, Shapiro Beth, Gilbert M Thomas P
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.
McBride Alan J A, Cerqueira Gustavo M, Suchard Marc A, Moreira Angela N, Zuerner Richard L, Reis Mitermayer G, Haake David A, Ko Albert I, Dellagostin Odir A
Genetic diversity of the Leptospiral immunoglobulin-like (Lig) genes
in pathogenic Leptospira spp
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases,
2009; 9(2):
196-205.
Seeram Navindra P, Zhang Yanjun, McKeever Rodney, Henning Susanne M, Lee Ru-po, Suchard Marc A, Li Zhaoping, Chen Steve, Thames Gail, Zerlin Alona, Nguyen Martha, Wang David, Dreher Mark, Heber David
Pomegranate juice and extracts provide similar levels of plasma and
urinary ellagitannin metabolites in human subjects
Journal of medicinal food,
2008; 11(2):
390-4.
Stevenson Brian, Choy Henry A, Pinne Marija, Rotondi Matthew L, Miller M Clarke, Demoll Edward, Kraiczy Peter, Cooley Anne E, Creamer Trevor P, Suchard Marc A, Brissette Catherine A, Verma Ashutosh, Haake David A
Leptospira interrogans endostatin-like outer membrane proteins bind
host fibronectin, laminin and regulators of complement
PloS one,
2007; 2(11):
e1188.
Seeram Navindra P, Aronson William J, Zhang Yanjun, Henning Susanne M, Moro Aune, Lee Ru-Po, Sartippour Maryam, Harris Diane M, Rettig Matthew, Suchard Marc A, Pantuck Allan J, Belldegrun Arie, Heber David
Pomegranate ellagitannin-derived metabolites inhibit prostate cancer
growth and localize to the mouse prostate gland
Journal of agricultural and food chemistry,
2007; 55(19):
7732-7.
Liao Joseph C, Mastali Mitra, Li Yang, Gau Vincent, Suchard Marc A, Babbitt Jane, Gornbein Jeffrey, Landaw Elliot M, McCabe Edward R B, Churchill Bernard M, Haake David A
Development of an advanced electrochemical DNA biosensor for bacterial
pathogen detection
The Journal of molecular diagnostics : JMD,
2007; 9(2):
158-68.
Liao Joseph C, Mastali Mitra, Gau Vincent, Suchard Marc A, Møller Annette K, Bruckner David A, Babbitt Jane T, Li Yang, Gornbein Jeffrey, Landaw Elliot M, McCabe Edward R B, Churchill Bernard M, Haake David A
Use of electrochemical DNA biosensors for rapid molecular
identification of uropathogens in clinical urine specimens
Journal of clinical microbiology,
2006; 44(2):
561-70.