List of works - Aris Katzourakis

'There and back again': revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era

scientific article

A contaminant-free assessment of Endogenous Retroviral RNA in human plasma

scientific article

A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data.

scientific article published on July 2017

A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution

scientific article

Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4.

scientific article published on 02 February 2009

B-cell depletion reveals a role for antibodies in the control of chronic HIV-1 infection

scientific article

BlastAlign: a program that uses blast to align problematic nucleotide sequences.

scientific article

Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences

scientific article published on 18 June 2008

Convergent capture of retroviral superantigens by mammalian herpesviruses

scientific article

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

scientific article

Detecting natural selection in RNA virus populations using sequence summary statistics

scientific article published on 11 June 2009

Discovery and analysis of the first endogenous lentivirus

scientific article (publication date: 10 April 2007)

Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution

scientific article

Disease-associated XMRV sequences are consistent with laboratory contamination

scientific article

Disentangling the origins of virophages and polintons

scientific article published on 9 August 2017

Editorial overview: Paleovirology: the genomic fossil record, and consequences of ancient viral infections.

scientific article

Effects of recombination rate on human endogenous retrovirus fixation and persistence.

scientific article

Endogenous retroviruses.

scientific article published on August 2015

Endogenous viral elements in animal genomes

scientific article published in November 2010

Endogenous viruses: Connecting recent and ancient viral evolution

scientific article published on 12 March 2015

Env-less endogenous retroviruses are genomic superspreaders

scientific article

Evaluating phylogenetic tree shape: two modifications to Fusco & Cronk's method.

scientific article published in January 2002

Evolution: Endogenous Viruses Provide Shortcuts in Antiviral Immunity.

scientific article published on May 2016

HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification

scientific article published on 01 July 2020

HIV-infected sex workers with beneficial HLA-variants are potential hubs for selection of HIV-1 recombinants that may affect disease progression

scientific article published on 17 June 2015

HLA Footprints on Human Immunodeficiency Virus Type 1 Are Associated with Interclade Polymorphisms and Intraclade Phylogenetic Clustering

scholarly article by Philippa C Matthews et al published 15 April 2011 in Journal of Virology

HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering

scientific article published on 25 February 2009

High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to reinfection

scientific article

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

scientific article published on 19 February 2018

Human endogenous retrovirus (HERV) expression is not induced by treatment with the histone deacetylase (HDAC) inhibitors in cellular models of HIV-1 latency

scientific article published on 6 February 2016

Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses

scientific article (publication date: 5 February 2009)

Independent evolution of intracellular transposons from exogenous IAP-related retroviruses in a broad range of mammalian species.

scientific article published on 6 June 2011

Larger mammalian body size leads to lower retroviral activity

scientific article

Long-term reinfection of the human genome by endogenous retroviruses

scientific article

Macroevolution of complex retroviruses

scientific article published in September 2009

Macroevolution of hoverflies (Diptera: Syrphidae): the effect of using higher-level taxa in studies of biodiversity, and correlates of species richness

article

Marine origin of retroviruses in the early Palaeozoic Era

scientific article

Modular nature of simian foamy virus genomes and their evolutionary history

scientific article published on 01 July 2019

Molecular epidemiology reveals the role of war in the spread of HIV in Ukraine.

scientific article published on 16 January 2018

Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split

scientific article published on 20 June 2015

P07-09. Contemporaneous transmission of genetically distinct HIV variants from a single donor to two recipients.

scientific article published on 22 October 2009

Paleovirology of human endogenous retroviruses

scientific article (publication date: 2009)

Paleovirology reveals the macroevolution of complex retroviruses

scientific article published on 24 September 2009

Paleovirology: inferring viral evolution from host genome sequence data

scientific article (publication date: 19 September 2013)

Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved

scientific article

Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants

scientific article

Phylogenetic analysis of murine leukemia virus sequences from longitudinally sampled chronic fatigue syndrome patients suggests PCR contamination rather than viral evolution.

scientific article

Prevalence of HIV type-1 drug-associated mutations in pre-therapy patients in the Free State, South Africa

scientific article published in January 2009

Proceedings of the Frontiers of Retrovirology Conference 2016.

scientific article published on 26 September 2016

Rate of recombinational deletion among human endogenous retroviruses

scientific article published on 20 June 2007

Reducing HIV infection in people who inject drugs is impossible without targeting recently-infected subjects.

scientific article

Roles of Endogenous Retroviruses in Early Life Events.

scientific article

STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data

scientific article published on July 2017

Sex-specific aspects of endogenous retroviral insertion and deletion

scientific article

Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface

scientific article

The First Co-Opted Endogenous Foamy Viruses and the Evolutionary History of Reptilian Foamy Viruses

scientific article published on 12 July 2019

The evolutionary dynamics of endogenous retroviruses

scientific article

The first endogenous herpesvirus, identified in the tarsier genome, and novel sequences from primate rhadinoviruses and lymphocryptoviruses

scientific article (publication date: June 2014)

The global spread of HIV-1 subtype B epidemic

scientific article

The mode and tempo of hepatitis C virus evolution within and among hosts ⬇️

scientific article

The origins of giant viruses, virophages and their relatives in host genomes

scientific article

Time dependency of foamy virus evolutionary rate estimates

scientific article

Time-Dependent Rate Phenomenon in Viruses

scientific article

Upregulation of Human Endogenous Retroviruses in Bronchoalveolar Lavage Fluid of COVID-19 Patients

scientific article published on 15 May 2020

Wide distribution and ancient evolutionary history of simian foamy viruses in New World primates

scientific article

List of works by Aris Katzourakis

'There and back again': revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era

A contaminant-free assessment of Endogenous Retroviral RNA in human plasma

A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data.

A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution

Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4.

B-cell depletion reveals a role for antibodies in the control of chronic HIV-1 infection

BlastAlign: a program that uses blast to align problematic nucleotide sequences.

Conserved footprints of APOBEC3G on Hypermutated human immunodeficiency virus type 1 and human endogenous retrovirus HERV-K(HML2) sequences

Convergent capture of retroviral superantigens by mammalian herpesviruses

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

Detecting natural selection in RNA virus populations using sequence summary statistics

Discovery and analysis of the first endogenous lentivirus

Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution

Disease-associated XMRV sequences are consistent with laboratory contamination

Disentangling the origins of virophages and polintons

Editorial overview: Paleovirology: the genomic fossil record, and consequences of ancient viral infections.

Effects of recombination rate on human endogenous retrovirus fixation and persistence.

Endogenous retroviruses.

Endogenous viral elements in animal genomes

Endogenous viruses: Connecting recent and ancient viral evolution

Env-less endogenous retroviruses are genomic superspreaders

Evaluating phylogenetic tree shape: two modifications to Fusco & Cronk's method.

Evolution: Endogenous Viruses Provide Shortcuts in Antiviral Immunity.

HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification

HIV-infected sex workers with beneficial HLA-variants are potential hubs for selection of HIV-1 recombinants that may affect disease progression

HLA Footprints on Human Immunodeficiency Virus Type 1 Are Associated with Interclade Polymorphisms and Intraclade Phylogenetic Clustering

HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering

High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to reinfection

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

Human endogenous retrovirus (HERV) expression is not induced by treatment with the histone deacetylase (HDAC) inhibitors in cellular models of HIV-1 latency

Identification of a RELIK orthologue in the European hare (Lepus europaeus) reveals a minimum age of 12 million years for the lagomorph lentiviruses

Independent evolution of intracellular transposons from exogenous IAP-related retroviruses in a broad range of mammalian species.

Larger mammalian body size leads to lower retroviral activity

Long-term reinfection of the human genome by endogenous retroviruses

Macroevolution of complex retroviruses

Macroevolution of hoverflies (Diptera: Syrphidae): the effect of using higher-level taxa in studies of biodiversity, and correlates of species richness

Marine origin of retroviruses in the early Palaeozoic Era

Modular nature of simian foamy virus genomes and their evolutionary history

Molecular epidemiology reveals the role of war in the spread of HIV in Ukraine.

Orthologous endogenous retroviruses exhibit directional selection since the chimp-human split

P07-09. Contemporaneous transmission of genetically distinct HIV variants from a single donor to two recipients.

Paleovirology of human endogenous retroviruses

Paleovirology reveals the macroevolution of complex retroviruses

Paleovirology: inferring viral evolution from host genome sequence data

Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved

Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants

Phylogenetic analysis of murine leukemia virus sequences from longitudinally sampled chronic fatigue syndrome patients suggests PCR contamination rather than viral evolution.

Prevalence of HIV type-1 drug-associated mutations in pre-therapy patients in the Free State, South Africa

Proceedings of the Frontiers of Retrovirology Conference 2016.

Rate of recombinational deletion among human endogenous retroviruses

Reducing HIV infection in people who inject drugs is impossible without targeting recently-infected subjects.

Roles of Endogenous Retroviruses in Early Life Events.

STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data

Sex-specific aspects of endogenous retroviral insertion and deletion

Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface

The First Co-Opted Endogenous Foamy Viruses and the Evolutionary History of Reptilian Foamy Viruses

The evolutionary dynamics of endogenous retroviruses

The first endogenous herpesvirus, identified in the tarsier genome, and novel sequences from primate rhadinoviruses and lymphocryptoviruses

The global spread of HIV-1 subtype B epidemic

The mode and tempo of hepatitis C virus evolution within and among hosts ⬇️

The origins of giant viruses, virophages and their relatives in host genomes

Time dependency of foamy virus evolutionary rate estimates

Time-Dependent Rate Phenomenon in Viruses

Upregulation of Human Endogenous Retroviruses in Bronchoalveolar Lavage Fluid of COVID-19 Patients

Wide distribution and ancient evolutionary history of simian foamy viruses in New World primates