2012

Gray RR, Salemi M, Klenerman P, Pybus OG. A new evolutionary model for hepatitis C virus chronic infection. PLoS Pathogens In press

2011

RR Gray*, J Parker*, P Lemey, M Salemi, A Katzourakis, OG Pybus. The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evolutionary Biology 11:131

RR Gray, OG Pybus, M Salemi. Measuring the temporal structure in serially-sampled phylogenies. Methods in Ecology & Evolution 2:437-45

RR Gray, AJ Tatem, JA Johnson, AV Alekseyenko, OG Pybus, MA Suchard, M Salemi. Bayesian phylogenetics of bacterial genomes: inferring the pandemic spread of Methicillin resistant Staphylococcus aureus ST239. Molecular Biology & Evolution 28: 1593-1603

RR Gray, M Salemi, A Lowe, KJ Nakamura, WD Decker, M Sinkala, C Kankasa, CJ Mulligan, D Thea, L Kuhn, G Aldrovandi, MM Goodenow. Multiple independent lineages of HIV-1 persist in breast milk and plasma. AIDS 25:143-152

SL Lamers*, RR Gray*, M Salemi*, M McGrath. HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues. Infection, Genetics & Evolution 11:31-37 

S Strickland*, RR Gray*, S Lamers, T Burdo, E Huenink, D Nolan, B Nowlin, X Alvarez, C Midkiff, MM Goodenow, K Williams, M Salemi. Significant genetic heterogeneity of the SIVmac251 viral swarm derived from different sources. AIDS Research and Human Retroviruses 27:1327-32

NM Véras, RR Gray, LF Brígido, R Rodrigues, M Salemi. High-resolution phylogenetics and phylogeography of HIV-1 subtype C epidemic in South America. Journal of General Virology 92:1698-709

C Massimo, AR Ciccaglione, A Lo Presti, T Yalcinkaya, M Equestre, A Costantino, R Bruni, E Ebranati, M Salemi, RR Gray, G Rezza, M Galli, G Zehende. Reconstruction of the evolutionary dynamics of the hepatitis C virus 1b epidemic in Turkey. Infection, Genetics & Evolution 11:863-8

M Prosperi, M Ciccozzi, I Fanti, F  Saladini, M Pecorari, V Borghi, S Di Giambenedetto, B Bruzzone, A Capetti, A Vivarelli, S Rusconi, M Carla Re, MR Gismondo, L Sighinolfi, RR Gray, M Salemi, M Zazzi, A De Luca. A novel methodology for large-scale phylogeny partition. Nature Communications 2:321

NM Véras, MM Santoro, RR Gray, AJ Tatem, A Lo Presti, F Olearo, G Cappelli, V Colizzi, D Takou, J Torimiro, G Russo, A Callegaro, R Salpini, R D'Arrigo, CF Perno, MM Goodenow, M Ciccozzi, M Salemi. Molecular Epidemiology of HIV-1 CRF02_AG in Cameroon and African Patients Living in Italy. AIDS Research Human Retroviruses 27:1173-82

J Liu, Z Zhou, CA Hodgkinson, Q Yuan, PH Shen, CJ Mulligan, A Wang, RR Gray, A Roy, M Virkkunen, D Goldman, MA Enoch. Haplotype-Based Study of the Association of Alcohol Metabolizing Genes with Alcohol Dependence in Four Independent Populations. Alcoholism: Clinical and Experimental Research 35:1-13

2010

RR Gray, NMC Veras, LA Santos, M Salemi. Evolutionary characterization of the West Nile virus complete genome. Molecular Phylogenetics & Evolution 56:195-200

M Salemi, SL Lamers, LC Huysentruyt, D Galligan, RR Gray, A Morris, MS McGrath. Distinct patterns of HIV-1 evolution within metastatic tissues in patients with non-Hodgkins lymphoma. PLoS One 4:e8153

SL Lamers, M Salemi, DC Galligan, A Morris, RR Gray, G Fogel, T de Oliveria, L Zhao, MS McGrath. HIV evolution within the brain: pathogenic processes define differences in viral evolutionary patterns. Journal of Neurovirology 16:230-241

2009

RR Gray, AJ Tatem, S Lamers, O Laeyendecker, D Serwadda, N Sewankambo, RH Gray, M Wawer, TC Quinn, W Hou, MM Goodenow, M Salemi. Spatial phylodynamics of HIV-1 epidemic emergence in east Africa. AIDS 23:F9-17

WM Switzer, M Salemi, SH Qari, H Jia, RR Gray, A Katzourakis, SJ Marriott, KN Pryor, ND Wolfe, DS Burke, TM Folks, W Heneine. Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4. Retrovirology 6:9

2008

M Salemi, RR Gray, MM Goodenow. A fast and reliable method for detecting intra-patient recombination. Molecular Phylogenetics & Evolution 49:618-628

2007

M Salemi, BR Burkhardt, RR Gray, G Ghaffari, JW Sleasman, MM Goodenow. Phylodynamics of HIV-1 in lymphoid and non-lymphoid tissues reveals a central role for the thymus in emergence of CXCR4-Using quasispecies. PLoS One 2:e950

J Clarimon*, RR Gray*, L Williams, MA Enoch, R Robin, B Albaugh, A Singleton, D Goldman, CJ Mulligan. Linkage disequilibrium and association analysis of alpha synuclein (SNCA) and alcohol and drug dependence in two American Indian populations. Alcoholism: Clinical and Experimental Research 4:1-9

2006

RR Gray, CJ Mulligan, BJ Molini, ES Sun, L Giacani, C Godornes, A Kitchen, SA Lukehart, A Centurion-Lara. Molecular evolution of the tprC, D, I, K, G, and J genes in the pathogenic genus Treponema. Molecular Biology & Evolution 23:2220-2233

L Tarskaia, RR Gray, B Burkley, CJ Mulligan. Genetic variation at the mitochondrial 9-bp repeat locus in the Sakha of Siberia. Human Biology 78:179-198

Room D59

Department of Zoology

University of Oxford

South Parks Road

Oxford

OX1 3PS, UK

(Email)

My research interests involve understanding the complexity of interactions between pathogens and a heterogeneous environment. In particular, my work focuses on developing models to find ecological associations and predictors of infectious disease epidemics. This framework can be applied to multiple scales of analysis, from the global scale of pandemics to a single host organism. Specific biological questions that intrigue me include the evolutionary behaviour of the hepatitis C virus within individuals over time, and the impact of modern farming practices on the emergence and spread of viral diseases.