Publications

Katzourakis A. (2017) Editorial Overview: Paleovirology: the genomic fossil record, and consequences of ancient viral infections 25: ix-xi

Aswad A, Katzourakis A. (2017) A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data. Virus Evolution 3(2):vex016

Magiorkinis G, Katzourakis A, Lagiou P. (2017) Roles of endogenous retroviruses in early life events. Trends in Microbiology 25(11): 876-877

Santander CG, Gambron P, Marchi E, Karamitros T, Katzourakis A, Magiorkinis G. (2017) STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data. Virus Evolution 3(2): vex023

Campbell S, Aswad A, Katzourakis A. (2017) Disentangling the origins of virophages and polintons. Current Opinion in Virology 25:59-65

Aiewsakun P, Katzourakis A. (2017) Marine origin of retroviruses in the early paleozoic era. Nature Communications 8:13954

Aiewsakun P, Katzourakis A. (2016) Time-dependent rate phenomenon in viruses. Journal of Virology 90(16):7184-95

Gemmell P, Hein J, Katzourakis A. (2016) Phylogenetic analysis reveals that ERVs “die young” but HERV-H is unusually conserved. PLoS Computational Biology 12(6):e1004964

Katzourakis A, Aswad A. (2016) Evolution: Endogenous viruses provide shortcuts in antiviral immunity. Current Biology 26(10):R427-9

Karamitros T, Paraskevis D, Hatzakis, A, Psichogiou M, Elefsiniotis I, Hurst T, Gerretti AM, Beloukas A, Frater J, Klenerman P, Katzourakis A, Magiorkinis G. (2016) A contaminant-free assessment of endogenous retroviral RNA in human plasma. Scientific Reports 6:33598

Vasylyeva TI, Friedman SR, Lourenco J, Gupta S, Hatzakis A, Pybus OG, Katzourakis A, Smyrnov P, Karamitros T, Paraskevis D, Magiorkinis G. (2016) Reducing HIV infection in people who inject drugs is impossible without targeting recently-infected subjects. AIDS 30(18):2885-2890

Karamitros T, Harrison I, Piorkowska R, Katzourakis A, Magiorkinis G, Mbisa JL. (2016) De Novo assembly of human herpes virus type 1 (HHV-1) genome, mining of non-canonical structures and detection of novel drug-resistance mutations using short- and long-read next generation sequencing technologies. PLoS ONE 11(6):e0157600

Magiorkinis G, Angelis K, Mamais I, Katzourakis A, et al [50 authors in total]. (2016) The global spread of HIV-1 subtype B epidemic. Infection Genetics and evolution S1567-1348(16)30223-4

Hurst T, Pace M, Katzourakis A, Phillips R, Klenerman P, Frater J, Magiorkinis G. (2016) Human endogenous retrovirus (HERV) exptression is not induced by treatment with the histone deacetylase (HDAC) inhibitors in cellular models of HIV-1 latency. Retrovirology 13:10

Aswad A, Katzourakis A. (2016) Paleovirology: The study of endogenous viral elements. Book chapter in ‘Virus Evolution’ (SC Weaver, MR Denison, M Roossinck M Vignuzzi eds), Horizon press

Mourikis A, Aswad A, Katzourakis A. (2016) Endogenous retroviruses and coevolution. Book chapter in ‘Encyclopedia of evolutionary biology’ (R Kliman eds), Elsevier

Aswad A, Katzourakis A. (2015) Convergent capture of retroviral superantigens by mammalian herpesviruses. Nature Communications 6:8299. (Covered in News & Analysis article in Nature Reviews Microbiology by Astrid Gall).

Hayward A, Katzourakis A. (2015) Quick guide: Endogenous retroviruses. Current Biology 15:R644-R646

Aiewsakun P, Katzourakis A. (2015) Time dependency of foamy virus evolutionary rate estimates. BMC Evolutionary Biology 15:119

Gemmell P, Hein J, Katzourakis A. (2015) Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split. Retrovirology 13:243

Aiewsakun P, Katzourakis A, (2015) Endogenous viruses: connecting recent and ancient viral evolution. Virology 479-480:26-37

Ghersi BM, Jia H, Aiewsakun P, Katzourakis A, Mendoza P, Bausch DG, Kasper MR, Montgomery JM, Switzer WM. (2015). Wide distribution and ancient evolutionary history of simian foamy viruses in New World primates. Retrovirology 12:89

Chang C-H, Kist NC, Stuart Chester TL, Sreenu VB, Herman M, Luo M, Lunn D, Bell J, Plummer FA, Blake Ball T, Katzourakis A, Iversen AK. (2015) HIV-infected sex workers with beneficial HLA-variants are potential hubs for selection of HIV-1 recombinants that may affect disease progression. Scientific Reports 5:11253

Aswad A, Katzourakis A. (2014) The first endogenous herpesvirus, identified in the tarsier genome, and novel sequences from primate rhadinoviruses and lymphocryptoviruses. PLoS Genetics 10:e1004332

Katzourakis A, Aiewsakun P, Jia H, Wolfe N, LeBreton M, Yoder A, Switzer WM. (2014) Discovery of prosimian and afrotherian foamy viruses reveals rare host switching amidst stable and ancient mammalian co-evolution. Retrovirology 11:61

Katzourakis A, Magiorkinis G, Lim A, Gupta S, Belshaw R, Gifford RJ. (2014) Larger mammalian body size leads to lower retroviral activity. PLoS Pathogens 10:e1004214 (covered by Science and Scientific American)

Katzourakis A, Aswad A (2014) The origins of giant viruses, virophages and their relatives in host genomes. BMC Biology 12:51

Gemmell P, Hein J, Katzourakis A. (2013) Sex-specific aspects of endogenous retroviral insertion and deletion. BMC Evolutionary Biology 13:243

Katzourakis A. (2013) Paleovirology: inferring viral evolution from host genome sequence data. Philosophical Transactions of the Royal Society Series B 368:20120493

Magiorkinis G, Belshaw R, Katzourakis A. (2013) ‘There and back again’: revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era. Philosophical Transactions of the Royal Society Series B 368:20120504

Aswad A, Katzourakis A. (2012) Paleovirology and virally derived immunity. Trends in Ecology and Evolution 27:627-36

Magiorkinis G, Gifford R, Katzourakis A, et al. (2012) Env-less endogenous retroviruses are genomic superspreaders. Proceedings of the National Academy of Sciences USA 109:7385-90

Katzourakis A, Hué S, Kellam P, Towers GJ. (2011) 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, et al. (2011) 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. (2011) The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evolutionary Biology 11:131

Katzourakis A, Gifford RJ. (2010) Endogenous viral elements in animal genomes. PLoS Genetics 6:e1001191. (Associated commentary in PLoS Genetics by Welkin Johnson)

Hué S, Gray ER, Gall A, Katzourakis A, et al. (2010) Disease-associated XMRV sequences are consistent with laboratory contamination. Retrovirology 7:111

Huang KH, Bonsall D, Katzourakis A, et al. (2010) 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. (2010) Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface. Cell Host Microbe 8:248-59

Bhatt S, Katzourakis A, Pybus OG. (2010) Detecting natural selection in RNA virus populations using sequence summary statistics. Infection Genetics & Evolution 10:421-30

Katzourakis A, Gifford, RJ, Tristem M, Gilbert MTP, Pybus OG. (2009) Macroevolution of complex retroviruses. Science 325:1512.

Huang K-H, Goedhals, D, Fryer, H, van Vuuren, C., Katzourakis, A., De Oliveira, T., Cassol, S., Seebregts, C., McLean, A. R., Klenerman, P., Phillips, R. E., Frater, J. (2009). Low CD4 cell counts are associated with pre-therapy HIV drug resistance. Antiviral Therapy 14 (7), 975-984

Matthews PC, Leslie AJ, Katzourakis A, Crawford H, Payne R, Prendergast A, Power K, Kelleher AD, Klenerman P, Carlson J, Heckerman D, Nudng’u T, Walker BD, Allen TM, Pybus OG, Goulder PJ. (2009). HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering. Journal of Virology 83: 4605-4615.

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.

Keckesova Z, Ylinen LMJ, Towers GJ, Gifford RJ, Katzourakis A. (2009). Identification of a RELIK orthologue in the genome of the European hare (Lepus Europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses. Virology 384: 7-11.

Gifford RJ $, Katzourakis A$, Tristem M, Pybus OG, Winters M, Shafer RW. (2008). 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: 20362-20367. (Associated commentary in PNAS by Welkin Johnson). ($ indicates equal contributions).

Armitage AE, Katzourakis A, de Oliveira T, Welch JJ, Belshaw R, Bishop KN, Kramer B, McMichael AJ, Rambaut A, Iversen AKN. (2008). Conserved footprints of APOBEC3G on hypermutated HIV-1 and HERV-K(HML2) sequences. Journal of Virology 82: 8743-8761.

Katzourakis A, Pereira V, Tristem M. (2007). Effects of recombination rate on human endogenous retrovirus fixation and persistence. Journal of Virology 81: 10712-10717. (Selected by Faculty of 1000).

Belshaw R, Watson J, Katzourakis A, Howe A, Woolven-Allen J, Burt A, Tristem M. (2007). Rate of recombinational deletion among human endogenous retroviruses. Journal of Virology 81: 9437-9442.

Katzourakis A, Tristem M, Pybus OG, Gifford RJ. (2007). Discovery and analysis of the first endogenous lentivirus. Proceedings of the National Academy of Sciences USA 104: 6261-6265. (Associated commentary in PNAS, Science News Magazine, and Selected by Faculty of 1000).

Katzourakis A, Rambaut A, Pybus OG. (2005). The evolutionary dynamics of endogenous retroviruses. Trends in Microbiology 13: 463-468.

Belshaw R, Katzourakis A, Paces J, Burt A, Tristem M. (2005). High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to re-infection. Molecular Biology and Evolution 22: 814-817.

Belshaw R, Katzourakis A. (2005). BlastAlign: a program that uses blast to align problematic nucleotide sequences. Bioinformatics 21 (1): 122-123.

Katzourakis A, Tristem M. (2005). Phylogeny of human endogenous and exogenous retroviruses. In: Retroviruses and primate genome evolution (E. D. Sverdlov, ed.). 186-203.

Belshaw R, Pereira V, Katzourakis A, Talbot G, Paces J, Burt A, Tristem M. (2004). Long-term reinfection of the human genome by endogenous retroviruses. Proceedings of the National Academy of Sciences USA 101: 4894-4899.

Purvis A, Katzourakis A, Agapow PM. (2002). Evaluating phylogenetic tree shape: Two modifications to Fusco & Cronk’s method. Journal of Theoretical Biology 214 (1): 99-103.

Katzourakis A, Purvis A, Azmeh S, Rotheray G, Gilbert F. (2001). 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.

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