2012

Magiorkinis G, Gifford R, Katzourakis A, De Ranter J, Belshaw R. Env-less endogenous retroviruses are genomic superspreaders. Proceedings of the National Academy of Sciences USA In press

2011

Katzourakis A, Hué S, Kellam P, Towers GJ. Phylogenetic analysis of murine leukemia virus sequences from longitudinally sampled chronic fatigue syndrome patients suggests PCR contamination rather than viral evolution. Journal of Virology 85:10909-13

English S, Katzourakis A, Bonsall D, Flanagan P, Duda A, Fidler S, Weber J, McClure M, SPARTAC Trial Investigators, Phillips R, Frater J. Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants. Retrovirology 8:54

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

2010

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

Hué S, Gray ER, Gall A, Katzourakis A, Tan CP, Houldcroft CJ, McLaren S, Pillay D, Futreal A, Garson JA, Pybus OG, Kellam P, Towers GJ. Disease-associated XMRV sequences are consistent with laboratory contamination. Retrovirology 7:111

Huang KH, Bonsall D, Katzourakis A, Thomson EC, Fidler SJ, Main J, Muir D, Weber JN, Frater AJ, Phillips RE, Pybus OG, Goulder PJ, McClure MO, Cooke GS, Klenerman P. B-cell depletion reveals a role for antibodies in the control of chronic HIV-1 infection. Nature Communications 1:102

Goldstone DC, Yap MW, Robertson LE, Haire LF, Taylor WR, Katzourakis A, Stoye JP, Taylor IA. Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface. Cell Host Microbe 8:248-59

Bhatt S, Katzourakis A, Pybus OG. Detecting natural selection in RNA virus populations using sequence summary statistics. Infection Genetics & Evolution 10:421-30

2009

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

Matthews PC, Leslie A, Katzourakis A, Pfafferott K, Power K, Kelleher AD, Carlson J, Heckerman D, Walker BD, Allen TM, Pybus OG, Goulder PJR. HLA footprints in HIV-1 gag are associated with phylogenetic clustering and clade-specific amino acid polymorphism. Journal of Virology 83:4605-15

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

Huang K-H, Goedhals D, Fryer H, van Vuuren C, Katzourakis A, De Oliveira T, Cassol S, Seebregts C, McLean AR, Klenerman P, Phillips RE, Frater J. Prevalence of HIV type-1 drug-associated mutations in pre-therapy patients in the Free State, South Africa. Antiviral Therapy 14:975-84

Switzer WM, Salemi M, Qari SH, Jia H, Gray RR, Katzourakis A, Marriott SJ, Pryor KN, Wolfe ND, Burke DS, Folks TM, Heneine W (2009) Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4. Retrovirology 6:9

2008

Gifford RJ, Katzourakis A, Tristem M, Pybus OG, Winters M, Shafer RW. 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

Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A, Iversen AK. Conserved footprints of APOBEC3G on hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences. Journal of Virology 82:8743-61

2007

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

Katzourakis A, Pereira V, Tristem M. Effects of recombination rate on human endogenous retrovirus fixation and persistence. Journal of Virology 81:10712-7

Belshaw R, Watson J, Katzourakis A, Howe A, Woolven-Allen J, Burt A, Tristem M. Rate of recombinational deletion among human endogenous retroviruses. Journal of Virology 81:9437-42

2005

Katzourakis A, Rambaut A, Pybus OG. The evolutionary dynamics of endogenous retroviruses. Trends in Microbiology 13:463-8

Belshaw R, Katzourakis A, Paces J, Burt A, Tristem M. High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to reinfection. Molecular Biology & Evolution 22:814-7

Katzourakis A, Tristem M.  Phylogeny of human endogenous and exogenous retroviruses. In: Retroviruses and primate genome evolution (E. D. Sverdlov, editor) p.186-203

Belshaw R, Katzourakis A. BlastAlign: a program that uses blast to align problematic nucleotide sequences. Bioinformatics 21:122-3

2004

Belshaw R, Pereira V, Katzourakis A, Talbot G, Paces J, Burt A, Tristem M. Long-term reinfection of the human genome by endogenous retroviruses. Proceedings of the National Academy of Sciences USA 101:4894-9

2002

Purvis A, Katzourakis A, Agapow PM. Evaluating phylogenetic tree shape: two modifications to Fusco & Cronk's method. Journal of Theoretical Biology 214:99-103

2001

Katzourakis A, Purvis A, Azmeh S, Rotheray G, Gilbert F.  Macroevolution of hoverflies (Diptera: Syrphidae): the effect of using higher taxa in studies of biodiversity, and correlates of species richness.  Journal of Evolutionary Biology 14: 219-227

Room E111

Department of Zoology

University of Oxford

South Parks Road

Oxford

OX1 3PS, UK

(Email)

My research interests include genome evolution, viral evolution and mobile genetic element evolution. I am particularly interested in retroviruses, such as the endogenous retroviruses that constitute a substantial fraction of vertebrate genomes, and exogenous retroviruses such as HIV. My research primarily involves using gene sequence data to address evolutionary questions such as why certain retroviruses are more likely to cross species boundaries than others, what host factors affect retroviral activity, and many others. I am also interested in methods of evolutionary inference from gene sequence data.