Dr Robert Gifford

  • Research Bioinformatician / Evolutionary Biologist (Centre for Virus Research)

Research interests

CVR logo 

Viral Genomics & Bioinformatics
Paleovirology

My research addresses the ecology and evolution of viruses. Viruses typically have high mutation rates and can evolve extremely rapidly, yet may be the oldest of all kingdoms of life. We are still only just beginning to comprehend the extent and complexity of viral biodiversity, and to appreciate the myriad roles that viruses play as dynamic components of ecosystems. Over recent years, however, revolutionary advances in DNA sequencing and related information technologies have radically transformed the research landscape. As well as facilitating the use of genetic approaches to track viral evolution within and spread between infected hosts, explosive progress in genomics is allowing unprecedented insight into the longer-term history of viral evolution.

My principal contention is that understanding the long-term evolution and origins of viral species will allow the threat posed by contemporary viruses to be assessed and countered more effectively. A central theme in my research is the development of theories that link our growing understanding of contemporary viruses with ecological and evolutionary phenomena that took place over timescales ranging from hundreds to millions of years.


Publications

List by: Type | Date

Jump to: 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2009 | 2008
Number of items: 31.

2019

Valencia-Herrera, I., Faunes, F., Cena-Ahumada, E., Ibarra-Karmy, R., Gifford, R. J. and Arriagada, G. (2019) Molecular properties and evolutionary origins of a parvovirus-derived myosin fusion gene in guinea pigs. Journal of Virology, 93(17), e00404-19. (doi:10.1128/JVI.00404-19) (PMID:31217242)

Pénzes, J. J., de Souza, W. M., Agbandje-McKenna, M. and Gifford, R. J. (2019) An ancient lineage of highly divergent parvoviruses infects both vertebrate and invertebrate hosts. Viruses, 11(6), 525. (doi:10.3390/v11060525) (PMID:31174309) (PMCID:PMC6631224)

Singer, J. B. et al. (2019) Interpreting viral deep sequencing data with GLUE. Viruses, 11(4), 323. (doi:10.3390/v11040323) (PMID:30987147) (PMCID:PMC6520954)

Dennis, T. P.W., Souza, W. M. d., Marsile-Medun, S., Singer, J. B., Wilson, S. J. and Gifford, R. J. (2019) The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. Virus Research, 262, pp. 15-23. (doi:10.1016/j.virusres.2018.03.014) (PMID:29601845) (PMCID:PMC6372831)

2018

Singer, J. B., Thomson, E. C. , McLauchlan, J. , Hughes, J. and Gifford, R. J. (2018) GLUE: a flexible software system for virus sequence data. BMC Bioinformatics, 19, 532. (doi:10.1186/s12859-018-2459-9) (PMID:30563445) (PMCID:PMC6299651)

Zhu, H., Gifford, R. and Murcia, P. R. (2018) Distribution, diversity and evolution of endogenous retroviruses in perissodactyl genomes. Journal of Virology, 92(23), e00927-18. (doi:10.1128/JVI.00927-18) (PMID:30209175) (PMCID:PMC6232481)

Gifford, R. J. , Blomberg, J., Coffin, J. M., Fan, H., Heidmann, T., Mayer, J., Stoye, J., Tristem, M. and Johnson, W. E. (2018) Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology, 15, 59. (doi:10.1186/s12977-018-0442-1) (PMID:30153831) (PMCID:PMC6114882)

Dennis, T. P.W., Flynn, P. J., Souza, W. M. d., Singer, J. B., Moreau, C. S., Wilson, S. J. and Gifford, R. J. (2018) Insights into circovirus host range from the genomic fossil record. Journal of Virology, 92(16), e00145-18. (doi:10.1128/JVI.00145-18) (PMID:29875243) (PMCID:PMC6069186)

Pénzes, J. J., Marsile-Medun, S., Agbandje-McKenna, M. and Gifford, R. J. (2018) Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses. Virus Evolution, 4(2), vey026. (doi:10.1093/ve/vey026) (PMID:30443409) (PMCID:PMC6232428)

Cowton, V. M., Singer, J. B., Gifford, R. J. and Patel, A. H. (2018) Predicting the effectiveness of hepatitis C virus neutralizing antibodies by bioinformatic analysis of conserved epitope residues using public sequence data. Frontiers in Immunology, 9, 1470. (doi:10.3389/fimmu.2018.01470) (PMID:30013555) (PMCID:PMC6036255)

Krupovic, M. et al. (2018) Ortervirales: a new viral order unifying five families of reverse-transcribing viruses. Journal of Virology, 92(12), e00515-18. (doi:10.1128/JVI.00515-18) (PMID:29618642)

Blanco-Melo, D., Gifford, R. J. and Bieniasz, P. D. (2018) Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. Retrovirology, 15, 34. (doi:10.1186/s12977-018-0416-3) (PMID:29716624) (PMCID:PMC5930517)

Hron, T., Farkašová, H., Gifford, R. J. , Benda, P., Hulva, P., Görföl, T., Pačes, J. and Elleder, D. (2018) Remnants of an ancient deltaretrovirus in the genomes of horseshoe aats (Rhinolophidae). Viruses, 10(4), 185. (doi:10.3390/v10040185) (PMID:29642581) (PMCID:PMC5923479)

de Souza, W. M. et al. (2018) Novel parvoviruses from wild and domestic animals in Brazil provide new insights into parvovirus distribution and diversity. Viruses, 10(4), 143. (doi:10.3390/v10040143) (PMID:29565808) (PMCID:PMC5923437)

2017

Shaw, A. E. et al. (2017) Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses. PLoS Biology, 15(12), e2004086. (doi:10.1371/journal.pbio.2004086) (PMID:29253856) (PMCID:PMC574750)

Niebel, M., Singer, J. B., Nickbakhsh, S., Gifford, R. J. and Thomson, E. C. (2017) Hepatitis C and the absence of genomic data in low-income countries: a barrier on the road to elimination? Lancet Gastroenterology and Hepatology, 2(10), pp. 700-701. (doi:10.1016/S2468-1253(17)30257-1) (PMID:28895545)

Blanco-Melo, D., Gifford, R. J. and Bieniasz, P. D. (2017) Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors. eLife, 6, e22519. (doi:10.7554/eLife.22519) (PMID:28397686) (PMCID:PMC5388530)

Farkašová, H., Hron, T., Pačes, J., Hulva, P., Benda, P., Gifford, R. J. and Elleder, D. (2017) Discovery of an endogenous Deltaretrovirus in the genome of long-fingered bats (Chiroptera: Miniopteridae). Proceedings of the National Academy of Sciences of the United States of America, 114(12), pp. 3145-3150. (doi:10.1073/pnas.1621224114) (PMID:28280099) (PMCID:PMC5373376)

Henzy, J. E., Gifford, R. J. , Kenaley, C. P. and Johnson, W. E. (2017) An intact retroviral gene conserved in spiny-rayed fishes for over 100 My. Molecular Biology and Evolution, 34(3), pp. 634-639. (doi:10.1093/molbev/msw262) (PMID:28039384)

de Souza, W. M., Romeiro, M. F., Modha, S. , de Araujo, J., Queiroz, L. H., Durigon, E. L., Moraes Figueiredo, L. T., Murcia, P. R. and Gifford, R. (2017) Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution. Journal of General Virology, 98(2), pp. 225-229. (doi:10.1099/jgv.0.000671) (PMID:28284244) (PMCID:PMC5646239)

2016

Jacobs, M. et al. (2016) Late Ebola virus relapse causing meningoencephalitis: a case report. Lancet, 388(10043), pp. 498-503. (doi:10.1016/S0140-6736(16)30386-5) (PMID:27209148) (PMCID:PMC4967715)

Wu, H. L. et al. (2016) Identification and spontaneous immune targeting of an endogenous retrovirus K envelope protein in the Indian rhesus macaque model of human disease. Retrovirology, 13, 6. (doi:10.1186/s12977-016-0238-0) (PMID:26767784) (PMCID:PMC4714462)

2015

Ng, M. et al. (2015) Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats. eLife, 4, e11785. (doi:10.7554/eLife.11785) (PMID:26698106) (PMCID:PMC4709267)

2014

Henzy, J.E., Gifford, R.J. , Johnson, W.E. and Coffin, J. M. (2014) A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. Journal of Virology, 88(5), pp. 2398-2405. (doi:10.1128/JVI.02863-13)

Arriagada, G. and Gifford, R. J. (2014) Parvovirus-derived endogenous viral elements in two South American rodent genomes. Journal of Virology, 89(20), pp. 12158-12162. (doi:10.1128/JVI.01173-14) (PMID:25078696)

Katzourakis, A., Magiorkinis, G., Lim, A. G., Gupta, S., Belshaw, R. and Gifford, R. (2014) Larger mammalian body size leads to lower retroviral activity. PLoS Pathogens, 10(7), e1004214. (doi:10.1371/journal.ppat.1004214)

2013

Niewiadomska, A.M. and Gifford, R.J. (2013) The extraordinary evolutionary history of the reticuloendotheliosis viruses. PLoS Biology, 11(8), e1001642. (doi:10.1371/journal.pbio.1001642)

Rihn, S.J. , Wilson, S.J. , Loman, N.J., Alim, M., Bakker, S.E., Bhella, D. , Gifford, R.J., Rixon, F.J. and Bieniasz, P.D. (2013) Extreme genetic fragility of the HIV-1 capsid. PLoS Pathogens, 9(6), e1003461. (doi:10.1371/journal.ppat.1003461) (PMID:23818857) (PMCID:PMC3688543)

2012

Magiorkinis, G., Gifford, R.J., Katzourakis, A., De Ranter, J. and Belshaw, R. (2012) Env-less endogenous retroviruses are genomic superspreaders. Proceedings of the National Academy of Sciences of the United States of America, 109(19), pp. 7385-7390. (doi:10.1073/pnas.1200913109)

2009

Katzourakis, A., Gifford, R.J., Tristem, M., Gilbert, M.T.P. and Pybus, O.G. (2009) Macroevolution of complex retroviruses. Science, 325(5947), p. 1512. (doi:10.1126/science.1174149)

2008

Gifford, R.J., Katzourakis, A., Tristem, M., Pybus, O.G., Winters, M. and Shafer, R.W. (2008) A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proceedings of the National Academy of Sciences of the United States of America, 105(51), pp. 20362-20367. (doi:10.1073/pnas.0807873105)

This list was generated on Sun Oct 20 10:52:40 2019 BST.
Jump to: Articles
Number of items: 31.

Articles

Valencia-Herrera, I., Faunes, F., Cena-Ahumada, E., Ibarra-Karmy, R., Gifford, R. J. and Arriagada, G. (2019) Molecular properties and evolutionary origins of a parvovirus-derived myosin fusion gene in guinea pigs. Journal of Virology, 93(17), e00404-19. (doi:10.1128/JVI.00404-19) (PMID:31217242)

Pénzes, J. J., de Souza, W. M., Agbandje-McKenna, M. and Gifford, R. J. (2019) An ancient lineage of highly divergent parvoviruses infects both vertebrate and invertebrate hosts. Viruses, 11(6), 525. (doi:10.3390/v11060525) (PMID:31174309) (PMCID:PMC6631224)

Singer, J. B. et al. (2019) Interpreting viral deep sequencing data with GLUE. Viruses, 11(4), 323. (doi:10.3390/v11040323) (PMID:30987147) (PMCID:PMC6520954)

Dennis, T. P.W., Souza, W. M. d., Marsile-Medun, S., Singer, J. B., Wilson, S. J. and Gifford, R. J. (2019) The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. Virus Research, 262, pp. 15-23. (doi:10.1016/j.virusres.2018.03.014) (PMID:29601845) (PMCID:PMC6372831)

Singer, J. B., Thomson, E. C. , McLauchlan, J. , Hughes, J. and Gifford, R. J. (2018) GLUE: a flexible software system for virus sequence data. BMC Bioinformatics, 19, 532. (doi:10.1186/s12859-018-2459-9) (PMID:30563445) (PMCID:PMC6299651)

Zhu, H., Gifford, R. and Murcia, P. R. (2018) Distribution, diversity and evolution of endogenous retroviruses in perissodactyl genomes. Journal of Virology, 92(23), e00927-18. (doi:10.1128/JVI.00927-18) (PMID:30209175) (PMCID:PMC6232481)

Gifford, R. J. , Blomberg, J., Coffin, J. M., Fan, H., Heidmann, T., Mayer, J., Stoye, J., Tristem, M. and Johnson, W. E. (2018) Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology, 15, 59. (doi:10.1186/s12977-018-0442-1) (PMID:30153831) (PMCID:PMC6114882)

Dennis, T. P.W., Flynn, P. J., Souza, W. M. d., Singer, J. B., Moreau, C. S., Wilson, S. J. and Gifford, R. J. (2018) Insights into circovirus host range from the genomic fossil record. Journal of Virology, 92(16), e00145-18. (doi:10.1128/JVI.00145-18) (PMID:29875243) (PMCID:PMC6069186)

Pénzes, J. J., Marsile-Medun, S., Agbandje-McKenna, M. and Gifford, R. J. (2018) Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses. Virus Evolution, 4(2), vey026. (doi:10.1093/ve/vey026) (PMID:30443409) (PMCID:PMC6232428)

Cowton, V. M., Singer, J. B., Gifford, R. J. and Patel, A. H. (2018) Predicting the effectiveness of hepatitis C virus neutralizing antibodies by bioinformatic analysis of conserved epitope residues using public sequence data. Frontiers in Immunology, 9, 1470. (doi:10.3389/fimmu.2018.01470) (PMID:30013555) (PMCID:PMC6036255)

Krupovic, M. et al. (2018) Ortervirales: a new viral order unifying five families of reverse-transcribing viruses. Journal of Virology, 92(12), e00515-18. (doi:10.1128/JVI.00515-18) (PMID:29618642)

Blanco-Melo, D., Gifford, R. J. and Bieniasz, P. D. (2018) Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. Retrovirology, 15, 34. (doi:10.1186/s12977-018-0416-3) (PMID:29716624) (PMCID:PMC5930517)

Hron, T., Farkašová, H., Gifford, R. J. , Benda, P., Hulva, P., Görföl, T., Pačes, J. and Elleder, D. (2018) Remnants of an ancient deltaretrovirus in the genomes of horseshoe aats (Rhinolophidae). Viruses, 10(4), 185. (doi:10.3390/v10040185) (PMID:29642581) (PMCID:PMC5923479)

de Souza, W. M. et al. (2018) Novel parvoviruses from wild and domestic animals in Brazil provide new insights into parvovirus distribution and diversity. Viruses, 10(4), 143. (doi:10.3390/v10040143) (PMID:29565808) (PMCID:PMC5923437)

Shaw, A. E. et al. (2017) Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses. PLoS Biology, 15(12), e2004086. (doi:10.1371/journal.pbio.2004086) (PMID:29253856) (PMCID:PMC574750)

Niebel, M., Singer, J. B., Nickbakhsh, S., Gifford, R. J. and Thomson, E. C. (2017) Hepatitis C and the absence of genomic data in low-income countries: a barrier on the road to elimination? Lancet Gastroenterology and Hepatology, 2(10), pp. 700-701. (doi:10.1016/S2468-1253(17)30257-1) (PMID:28895545)

Blanco-Melo, D., Gifford, R. J. and Bieniasz, P. D. (2017) Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors. eLife, 6, e22519. (doi:10.7554/eLife.22519) (PMID:28397686) (PMCID:PMC5388530)

Farkašová, H., Hron, T., Pačes, J., Hulva, P., Benda, P., Gifford, R. J. and Elleder, D. (2017) Discovery of an endogenous Deltaretrovirus in the genome of long-fingered bats (Chiroptera: Miniopteridae). Proceedings of the National Academy of Sciences of the United States of America, 114(12), pp. 3145-3150. (doi:10.1073/pnas.1621224114) (PMID:28280099) (PMCID:PMC5373376)

Henzy, J. E., Gifford, R. J. , Kenaley, C. P. and Johnson, W. E. (2017) An intact retroviral gene conserved in spiny-rayed fishes for over 100 My. Molecular Biology and Evolution, 34(3), pp. 634-639. (doi:10.1093/molbev/msw262) (PMID:28039384)

de Souza, W. M., Romeiro, M. F., Modha, S. , de Araujo, J., Queiroz, L. H., Durigon, E. L., Moraes Figueiredo, L. T., Murcia, P. R. and Gifford, R. (2017) Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution. Journal of General Virology, 98(2), pp. 225-229. (doi:10.1099/jgv.0.000671) (PMID:28284244) (PMCID:PMC5646239)

Jacobs, M. et al. (2016) Late Ebola virus relapse causing meningoencephalitis: a case report. Lancet, 388(10043), pp. 498-503. (doi:10.1016/S0140-6736(16)30386-5) (PMID:27209148) (PMCID:PMC4967715)

Wu, H. L. et al. (2016) Identification and spontaneous immune targeting of an endogenous retrovirus K envelope protein in the Indian rhesus macaque model of human disease. Retrovirology, 13, 6. (doi:10.1186/s12977-016-0238-0) (PMID:26767784) (PMCID:PMC4714462)

Ng, M. et al. (2015) Filovirus receptor NPC1 contributes to species-specific patterns of ebolavirus susceptibility in bats. eLife, 4, e11785. (doi:10.7554/eLife.11785) (PMID:26698106) (PMCID:PMC4709267)

Henzy, J.E., Gifford, R.J. , Johnson, W.E. and Coffin, J. M. (2014) A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. Journal of Virology, 88(5), pp. 2398-2405. (doi:10.1128/JVI.02863-13)

Arriagada, G. and Gifford, R. J. (2014) Parvovirus-derived endogenous viral elements in two South American rodent genomes. Journal of Virology, 89(20), pp. 12158-12162. (doi:10.1128/JVI.01173-14) (PMID:25078696)

Katzourakis, A., Magiorkinis, G., Lim, A. G., Gupta, S., Belshaw, R. and Gifford, R. (2014) Larger mammalian body size leads to lower retroviral activity. PLoS Pathogens, 10(7), e1004214. (doi:10.1371/journal.ppat.1004214)

Niewiadomska, A.M. and Gifford, R.J. (2013) The extraordinary evolutionary history of the reticuloendotheliosis viruses. PLoS Biology, 11(8), e1001642. (doi:10.1371/journal.pbio.1001642)

Rihn, S.J. , Wilson, S.J. , Loman, N.J., Alim, M., Bakker, S.E., Bhella, D. , Gifford, R.J., Rixon, F.J. and Bieniasz, P.D. (2013) Extreme genetic fragility of the HIV-1 capsid. PLoS Pathogens, 9(6), e1003461. (doi:10.1371/journal.ppat.1003461) (PMID:23818857) (PMCID:PMC3688543)

Magiorkinis, G., Gifford, R.J., Katzourakis, A., De Ranter, J. and Belshaw, R. (2012) Env-less endogenous retroviruses are genomic superspreaders. Proceedings of the National Academy of Sciences of the United States of America, 109(19), pp. 7385-7390. (doi:10.1073/pnas.1200913109)

Katzourakis, A., Gifford, R.J., Tristem, M., Gilbert, M.T.P. and Pybus, O.G. (2009) Macroevolution of complex retroviruses. Science, 325(5947), p. 1512. (doi:10.1126/science.1174149)

Gifford, R.J., Katzourakis, A., Tristem, M., Pybus, O.G., Winters, M. and Shafer, R.W. (2008) A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proceedings of the National Academy of Sciences of the United States of America, 105(51), pp. 20362-20367. (doi:10.1073/pnas.0807873105)

This list was generated on Sun Oct 20 10:52:40 2019 BST.

Grants

Grants and Awards listed are those received whilst working with the University of Glasgow.

  • The center for HIV/AIDS-related structural biology
    National Institutes of Health
    2017 - 2018
     
  • Quinquennial Core Funds
    Medical Research Council
    2016 - 2021
     


Visit the Gifford Group webpage

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