Robert J. Gifford

Aaron Diamond Assistant Professor at Rockefeller University

Aaron Diamond AIDS Research Center

455 1st Avenue, New York

rgifford@adarc.org

Research interests

I am interested in the ecology and evolution of viruses, the epidemiology of viral diseases, and the dynamics of host-virus systems. My research involves the use of molecular biological and bioinformatic approaches to investigate virus evolution across both long and short timescales.

It is an exciting time for research in this area. Rapid advances in gene sequencing technology, and the development of new computational and statistical methods of analysis, are making large scale, phylodynamic investigations of viral populations increasingly feasible. At the same time, whole genome sequencing of eukaryotic organisms is revealing a rich and diverse fossil record for viruses, which we have only just begun to explore.

Current lab members
Anna Maria Niewiadomska	Postdoc	aniewiad@adarc.org

Software

The Calibrated Population Resistance Tool: (CPR) : a web application for standardized genotypic estimation of transmitted HIV-1 drug resistance. [link]

Selected Publications

Paleovirology

Gifford RJ (2011) Viral Evolution in Deep Time - Lentiviruses and Mammals. Trends in Genetics 2012 Feb;28(2):89-100. [view]

Gifford RJ (2011) No trespassing: ancient BST2 deletion confers protection against simian immunodeficiency virus infection of humans. Hum Mutat. 2011 Nov;32(11) [view]

Katzourakis A. and RJ. Gifford (2010) Endogenous viral elements in animal genomes. PLoS Genetics 6(11): e1001191. [view]

Katzourakis A*, Gifford RJ*, Tristem M, Gilbert MTP, and OG. Pybus (2009) The macroevolution of complex retroviruses. Science 325:1512 [view]
* co-corresponding authors

Keckesova Z, Ylinen LM, Towers GJ, Gifford RJ, and A. Katzourakis (2009) Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology 5;384(1):7-11 [view]

Gifford RJ, Katzourakis A, Tristem M, Pybus, OG, Winters M, and RW. Shafer. (2008) A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. PNAS 105:20362-7 [view]

Katzourakis A, Tristem M, Pybus OG, and RJ. Gifford (2007) Discovery and analysis of the first endogenous lentivirus. PNAS 104: 6261-5 [view]

Gifford RJ. (2006) Evolution at the host-retrovirus interface. Bioessays 28:1153-6 [view]

Ylinen LM, Keckesova Z, Webb BL, Gifford RJ, Smith TP, and GJ. Towers (2006) Isolation of an active Lv1 gene from cattle indicates that tripartite motif protein-mediated innate immunity to retroviral infection is widespread among mammals. J Virol. 80(15):7332-8 [view]

Gifford RJ, Kabat P, Martin J, Lynch C, and M. Tristem. (2005) Evolution and distribution of class II-related endogenous retroviruses. J. Virol. 79:6478-86 [view]

Gifford RJ and M Tristem. (2003). The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 26:291-315

Genetic Epidemiology

Geographic structuring of global EIAV isolates: A single origin for New World strains? (2012) Capomaccio S, Cappelli K, Cook RF, Nardi F, Gifford R, Marenzoni ML, Passamonti F. Virus Res Feb; 163(2): 656-9 [view]

de Oliveira T, Pillay D and RJ. Gifford (2010) The HIV-1 subtype C epidemic in South America is linked to the United Kingdom. PLoS ONE. 5(2):e9311. [view]

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 [view]

Hue S, Gifford RJ, Dunn D, Fearnhill E, and D. Pillay. (2009) Demonstration of sustained drug-resistant HIV-1 lineages circulating amongst drug-naive individuals. J. Virol. Mar;83(6):2645-54. [view]

Gifford RJ, Rhee SY, Eriksson N, Liu TF, Kiuchi M, Das AK, and RW. Shafer.(2008) Sequence editing by Apolipoprotein B RNA-editing catalytic component and epidemiological surveillance of transmitted HIV-1 drug resistance. AIDS Mar 30;22(6):717-25 [view]

Rhee SY, Liu TF, Kiuchi M, Zioni R, Gifford RJ, Holmes SP, and RW. Shafer. (2008) Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors. Retrovirology Aug 7;5:74. [view]

Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme A, Kellam P, and D. Pillay. (2007). Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of HIV-1. J. Virol. 81:13050-6 [view]

Gifford R, de Oliveira T, Rambaut A, Myers RE, Gale CV, Dunn D, Shafer R, Vandamme AM, Kellam P, and D. Pillay D (2006) Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity. AIDS Jul 13;20(11):1521-9. [view]

Pillay D, Bhaskaran K, Jurriaans S, Prins M, Masquelier B, Dabis F, Gifford R, et al on behalf of the CASCADE collaboration (2006) The impact of transmitted drug resistance on the natural history of HIV infection and response to first-line therapy. AIDS Jan 2;20(1):21-8. [view]

Masquelier B, Bhaskaran K, Pillay D, Gifford R, et al on behalf of the CASCADE collaboration (2005) 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. Dec 15;40(5):505-11. [view]