2010

Katzourakis A, Gifford RJ. Endogenous viral elements in animal genomes. PLoS Genetics 6:e1001191

2009

Gifford RJ, Liu TF, Rhee SY, Kiuchi M, Hue S, Pillay D, Shafer RW. 2009. The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. Bioinformatics. 25:1197-8

Hue S, Gifford RJ, Dunn D, Fearnhill E, and D Pillay. Demonstration of sustained drug-resistant HIV-1 lineages circulating amongst drug-naive individuals. J. Virol. In press

Katzourakis A, Gifford RJ, Tristem M, Gilbert MTP, Pybus OG. The macroevolution of complex retroviruses. Science 325:1512

Brown AE, Gifford RJ, Clewley JP, Kucherer C, Masquelier, B, Porter K, Balotta, C, Back, NKT, Jorgensen LB, de Mendoza C, Bhaskaran K, Gill ON, Johnson AM, and D Pillay. Phylogenetic reconstruction of transmissions from individuals with acute HIV infection: towards more rigorous epidemiological definitions. JID 199:427-431

2008

Gifford RJ, Katzourakis A, Tristem M, Pybus, OG, Winters M, and RW Shafer. A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proceedings of the National Academy of Sciences USA 105:20362-7

Ylinen LMJ, Keckesova Z, Towers GJ, Gifford RJ, and A Katzourakis. The time scale of lentiviral evolution: identification of a RELIK orthologue in the genome of the European hare (Lepus europaeus). Virology. In press

Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, and RW Shafer. Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors. Retrovirology 5:74

Gifford RJ, Rhee SY, Eriksson N, Liu TF, Kiuchi M, Das AK, and RW Shafer. APOBEC-mediated sequence editing and epidemiological surveillance of transmitted HIV-1 drug resistance. AIDS 22:717-725

2007

Katzourakis A, Tristem M, Pybus OG, and RJ Gifford. Discovery and analysis of the first endogenous lentivirus. Proceedings of the National Academy of Sciences USA 104: 6261-5

Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme A, Kellam P, and D. Pillay. Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of HIV-1. Journal of Virology 81:13050-6

UK Collaborative Group on HIV Drug Resistance. Evidence of a decline in transmitted HIV-1 drug resistance in the United Kingdom. AIDS 21:1035-39

2006

Gifford RJ. Evolution at the host-retrovirus Interface. Bioessays 28:1153-6

Ylinen LMJ, Keckesova Z, Webb BLJ, Gifford RJ, Smith PLS and GJ Towers. Isolation of an active Lv1 gene from cattle indicates that tripartite motif protein mediated innate immunity to retroviral infection is widespread among mammals. Journal of Virology 80:7332-8

Gifford RJ, de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme A, Kellam P, and D. Pillay. Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. AIDS 20:1521-9

Gifford RJ, Kellam P, Dunn DT, and D Pillay. The impact of structural and functional constraints acting at the nucleic acid level on the evolution of drug resistance in HIV-1. Antiviral Therapy 11:S57

Bezemer D, de Ronde A, Prins M, Gifford RJ, Pillay D, Masquelier B, Fleury H, Dabis F, Back N, Jurriaans S, and L van der Hoek; CASCADE collaboration. Evolution of transmitted HIV-1 with drug resistance mutations in the absence of therapy: effects on CD4+ T-cell count and HIV-1 RNA load. Antiviral Therapy 11:173-8

Pillay D, Bhaskaran K, Jurriaans S, Prins M, Masquelier B, Dabis F, Gifford RJ, Nielsen C, Pedersen C, Balotta C, Rezza G, Ortiz M, Mendoza C, Kucherer C, Poggensee G, Gill J and K. Porter on behalf of the CASCADE collaboration. The impact of transmitted drug resistance on the natural history of HIV infection and response to first-line therapy. AIDS 20:21-28

2005

Gifford RJ, Kabat P, Martin J, Lynch C, and M. Tristem. Evolution and distribution of class II-related endogenous retroviruses. Journal of Virology 79:6478-86

Gifford RJ and D Pillay. Utilisation of HIV-1 subtype specific consensus sequences to explore treatment related mutational patterns within and between subtypes. Antiviral Therapy 10:S153

Masquelier B, Bhaskaran K, Pillay D, Gifford RJ, Balestre E et al. Prevalence of Transmitted HIV-1 Drug Resistance and the Role of Resistance Algorithms: Data From Seroconverters in the CASCADE Collaboration From 1987 to 2003. J. Acquir. Immune Defic. Syndr. 40:505-511

2003

Gifford RJ and M Tristem. The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 26:291-315

The Aaron Diamond AIDS Research Center

455 First Avenue, 7th Floor

New York, NY 10016

USA

Phone: +1 212 448 5056

(Email)

I am interested in the ecology and evolution of viruses, particularly retroviruses. My research involves the use of gene sequence data to investigate current, past and future trends in viral evolution.