Dr Joseph Hughes

  • Bioinformatician (Centre for Virus Research)

Research interests

CVR logo

Viral genomics & bioinformatics programme

I am an evolutionary biologist with a particular interest in the evolution of host-parasite interactions. With evolution as a guiding theoretical principle, I am attempting to discover how evolutionary forces have shaped the solutions that parasites and viruses have found to adapt to their hosts and how these adaptations have resulted in the huge diversity of pathogens.

My current research focuses on various aspects of evolution in human and animal viruses using the wealth of sequence data generated by high-throughput sequencers. My research focuses on the following areas:

  • Intra-host virus diversity and evolution
  • Transmission network and disease outbreak analysis
  • Virus phylogenetics, recombination and reassortment
  • Immunoinformatics of T-cell receptors
  • Visualisation of large and complex datasets


Collaborators

I am collaborating with researchers within the Centre for Virus Research (Pablo Murcia, Emma Thomson), researchers within the Institute of Biodiversity, Animal Health and Comparative Medicine (Roman Biek, Richard Reeve, Richard Orton) and researchers at Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy (Isabella Monne, Alice Fusaro)


Selected Publications


Past research

For details on my research and publications before working at the CVR:

http://darwin.zoology.gla.ac.uk/%7Ejhughes/index.html


Publications

List by: Type | Date

Jump to: 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2007
Number of items: 49.

2019

Modha, S. , Hughes, J. , Bianco, G., Ferguson, H. M. , Helm, B., Tong, L., Wilkie, G. S., Kohl, A. and Schnettler, E. (2019) Metaviromics reveals unknown viral diversity in the biting midge Culicoides impunctatus. Viruses, 11(9), 865. (doi:10.3390/v11090865)

Suárez, N. M. et al. (2019) Human cytomegalovirus genomes sequenced directly from clinical material: variation, multiple-strain infection, recombination and gene loss. Journal of Infectious Diseases, 220(5), pp. 781-791. (PMID:31050742) (PMCID:PMC6667795)

Rihn, S. J. et al. (2019) TRIM69 inhibits Vesicular Stomatitis Indiana Virus (VSIV). Journal of Virology, (Accepted for Publication)

Alamil, M., Hughes, J. , Berthier, K., Desbiez, C., Thébaud, G. and Soubeyrand, S. (2019) Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1775), 20180258. (PMID:31056055)

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)

Davis, C. et al. (2019) New highly diverse hepatitis C strains detected in sub‐Saharan Africa have unknown susceptibility to direct‐acting antiviral treatments. Hepatology, 69(4), pp. 1426-1441. (doi:10.1002/hep.30342) (PMID:30387174) (PMCID:PMC6492010)

Rezelj, V. V., Mottram, T. J., Hughes, J. , Elliott, R. M., Kohl, A. and Brennan, B. (2019) M segment-based minigenomes and virus-like particle assays as an approach to assess the potential of tick-borne Phlebovirus genome reassortment. Journal of Virology, 93(6), e02068-18. (doi:10.1128/JVI.02068-18) (PMID:30567991) (PMCID:PMC6401446)

Zhu, H. et al. (2019) Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds. PLoS Pathogens, 15(2), e1007531. (doi:10.1371/journal.ppat.1007531) (PMID:30731004) (PMCID:PMC6366691)

Maabar, M., Davison, A. J. , Vučak, M., Thorburn, F., Gunson, R., Palmarini, M. and Hughes, J. (2019) DisCVR: rapid viral diagnosis from high-throughput sequencing data. Virus Evolution, (Accepted for Publication)

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)

Mercuri, L., Thomson, E. C. , Hughes, J. and Karayiannis, P. (2018) Quasispecies changes with distinctive point mutations in the Hepatitis C virus internal ribosome entry site (IRES) derived from PBMCs and plasma. Advances in Virology, 2018, 4835252. (doi:10.1155/2018/4835252) (PMID:30581467) (PMCID:PMC6276526)

Dunlop, J. I. et al. (2018) Development of reverse genetics systems and investigation of host response antagonism and reassortment potential for Cache Valley and Kairi viruses, two emerging orthobunyaviruses of the Americas. PLoS Neglected Tropical Diseases, 12(10), e0006884. (doi:10.1371/journal.pntd.0006884) (PMID:30372452) (PMCID:PMC6245839)

Modha, S. , Thanki, A., Cotmore, S. F., Davison, A. J. and Hughes, J. (2018) ViCTree: an automated framework for taxonomic classification from protein sequences. Bioinformatics, 34(13), pp. 2195-2200. (doi:10.1093/bioinformatics/bty099) (PMID:29474519) (PMCID:PMC6022645)

Saucedo, B. et al. (2018) Ranavirus genotypes in the Netherlands and their potential association with virulence in water frogs (Pelophylax spp.). Emerging Microbes and Infections, 7(1), 56. (doi:10.1038/s41426-018-0058-5) (PMID:29615625) (PMCID:PMC5882854)

da Silva Filipe, A. et al. (2018) Reply to: "Reply to: 'Response to DAA therapy in the NHS England Early Access Programme for rare HCV subtypes from low and middle income countries'". Journal of Hepatology, 68(4), pp. 864-866. (doi:10.1016/j.jhep.2017.11.044) (PMID:29339112)

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)

da Silva Filipe, A. et al. (2017) Response to DAA therapy in the NHS England early access programme for rare HCV subtypes from low and middle income countries. Journal of Hepatology, 67(6), pp. 1348-1350. (doi:10.1016/j.jhep.2017.06.035) (PMID:28789880)

Saucedo, B., Hughes, J. , van Beurden, S. J., Suárez, N. M., Haenen, O. L.M., Voorbergen-Laarman, M., Gröne, A. and Kik, M. J.L. (2017) Complete genome sequence of Frog virus 3, isolated from a strawberry poison frog (Oophaga pumilio) imported from Nicaragua into the Netherlands. Genome Announcements, 5(35), e00863-17. (doi:10.1128/genomeA.00863-17) (PMID:28860243) (PMCID:PMC5578841)

Milani, A. et al. (2017) Vaccine immune pressure influences viral population complexity of avian influenza virus during infection. Veterinary Microbiology, 203, pp. 88-94. (doi:10.1016/j.vetmic.2017.02.016)

Rihn, S. J. , Foster, T. L., Busnadiego, I., Aziz, M. A., Hughes, J. , Neil, S. J.D. and Wilson, S. J. (2017) The envelope gene of transmitted HIV-1 resists a late interferon gamma-induced block. Journal of Virology, 91(7), e02254-16. (doi:10.1128/JVI.02254-16) (PMID:28100611) (PMCID:PMC5355616)

2016

Donald, C. L. et al. (2016) Full genome sequence and sfRNA interferon antagonist activity of Zika virus from Recife, Brazil. PLoS Neglected Tropical Diseases, 10(10), e0005048. (doi:10.1371/journal.pntd.0005048) (PMID:27706161) (PMCID:PMC5051680)

Franzo, G., Cortey, M., Segalés, J., Hughes, J. and Drigo, M. (2016) Phylodynamic analysis of porcine circovirus type 2: Methodological approach and datasets. Data In Brief, 8, pp. 549-552. (doi:10.1016/j.dib.2016.06.005) (PMID:27508215) (PMCID:PMC4962815)

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)

Franzo, G., Cortey, M., Segalés, J., Hughes, J. and Drigo, M. (2016) Phylodynamic analysis of porcine circovirus type 2 reveals global waves of emerging genotypes and the circulation of recombinant forms. Molecular Phylogenetics and Evolution, 100, pp. 269-280. (doi:10.1016/j.ympev.2016.04.028) (PMID:27114187)

Fusaro, A. et al. (2016) Unexpected interfarm transmission dynamics during a highly pathogenic avian influenza epidemic. Journal of Virology, 90(14), pp. 6401-6411. (doi:10.1128/jvi.00538-16) (PMID:27147741) (PMCID:PMC4936132)

Robinson, M. W., Hughes, J. , Wilkie, G. S., Swann, R. , Barclay, S. T., Mills, P. R., Patel, A. H. , Thomson, E. C. and McLauchlan, J. (2016) Tracking TCRß sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region. Frontiers in Immunology, 7, 131. (doi:10.3389/fimmu.2016.00131) (PMID:27092143) (PMCID:PMC4820669)

Orton, R.J. , Gu, Q., Hughes, J. , Maabar, M., Modha, S. , Vattipally, S. , Wilkie, G.S. and Davison, A. (2016) Bioinformatics tools for analysing viral genomic data. Revue scientifique et technique (International Office of Epizootics), 35(1), pp. 241-285. (doi:10.20506/rst.35.1.2432) (PMID:27217183)

Rijks, J. M. et al. (2016) Investigation of amphibian mortality events in wildlife reveals an on-going ranavirus epidemic in the North of the Netherlands. PLoS ONE, 11(6), e0157473. (doi:10.1371/journal.pone.0157473) (PMID:27315226) (PMCID:PMC4912076)

2015

Stewart, M. et al. (2015) Characterization of a second open reading frame in genome segment 10 of bluetongue virus. Journal of General Virology, 96(11), pp. 3280-3293. (doi:10.1099/jgv.0.000267) (PMID:26290332) (PMCID:PMC4806581)

Nomikou, K., Hughes, J. , Wash, R., Kellam, P., Breard, E., Zientara, S., Palmarini, M. , Biek, R. and Mertens, P. (2015) Widespread reassortment shapes the evolution and epidemiology of bluetongue virus following European invasion. PLoS Pathogens, 11(8), e1005056. (doi:10.1371/journal.ppat.1005056) (PMID:26252219) (PMCID:PMC4529188)

Tilston-Lunel, N. L., Hughes, J. , Olszanski Acrani, G., da Silva, D. E.A., Azevedo, R. S.S., Rodrigues, S. G., Vasconcelos, P. F.C., Nunes, M. R.T. and Elliott, R. M. (2015) Genetic analysis of members of the species Oropouche virus and identification of a novel M segment sequence. Journal of General Virology, 96(7), pp. 1636-1650. (doi:10.1099/vir.0.000108) (PMID:25735305) (PMCID:PMC4635451)

Abdelrahman, T., Hughes, J. , Main, J., McLauchlan, J. , Thursz, M. and Thomson, E. (2015) Reply. Hepatology, 61(4), p. 1438. (doi:10.1002/hep.27393) (PMID:25147121) (PMCID:PMC4407921)

Ardelrahman, T., Hughes, J. , Main, J., McLauchlan, J. , Thursz, M. and Thomson, E. (2015) Waiting time and transplantation for hepatocellular cancer: a balance between tempus fugit and carpe diem. Hepatology, 61(4), pp. 1438-1439. (doi:10.1002/hep.27434)

Beczkowski, P. M., Hughes, J. , Biek, R. , Litster, A., Willett, B. J. and Hosie, M. J. (2015) Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus (FIV). Journal of General Virology, 96(4), pp. 893-903. (doi:10.1099/vir.0.000035) (PMID:25535323) (PMCID:PMC4361796)

Abdelrahman, T., Hughes, J. , Main, J., McLauchlan, J. , Thursz, M. and Thomson, E. (2015) Next generation sequencing sheds light on the natural history of hepatitis C infection in patients that fail treatment. Hepatology, 61(1), pp. 88-97. (doi:10.1002/hep.27192) (PMID:24797101) (PMCID:PMC4303934)

Rihn, S. J. , Hughes, J. , Wilson, S. J. and Bieniasz, P. D. (2015) Uneven genetic robustness of HIV-1 integrase. Journal of Virology, 89(1), pp. 552-567. (doi:10.1128/JVI.02451-14)

Fusaro, A., Tassoni, L., Hughes, J. , Milani, A., Salviato, A., Schivo, A., Murcia, P. R. , Bonfanti, L., Cattoli, G. and Monne, I. (2015) Evolutionary trajectories of two distinct avian influenza epidemics: parallelisms and divergences. Infection, Genetics and Evolution, 34, pp. 457-466. (doi:10.1016/j.meegid.2015.05.020) (PMID:26003682)

Zhu, H., Hughes, J. and Murcia, P. R. (2015) Origins and evolutionary dynamics of H3N2 canine influenza virus. Journal of Virology, 89(10), pp. 5406-5418. (doi:10.1128/JVI.03395-14)

2014

Bęczkowski, P. M., Hughes, J. , Biek, R. , Litster, A., Willett, B. J. and Hosie, M. J. (2014) Feline immunodeficiency virus (FIV) env recombinants are common in natural infections. Retrovirology, 11(80), (doi:10.1186/s12977-014-0080-1) (PMID:25699660) (PMCID:PMC4180853)

Busnadiego, I. et al. (2014) Host and viral determinants of Mx2 antiretroviral activity. Journal of Virology, 88(14), pp. 7738-7752. (doi:10.1128/JVI.00214-14) (PMID:24760893) (PMCID:PMC4097781)

Jombart, T. et al. (2014) OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics, 7, pp. 28-34. (doi:10.1016/j.epidem.2014.04.003)

Monne, I. et al. (2014) Emergence of a highly pathogenic avian influenza virus from a low-pathogenic progenitor. Journal of Virology, 88(8), pp. 4375-4388. (doi:10.1128/JVI.03181-13)

2013

Varela, M. et al. (2013) Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in Rhesus Macaques. PLoS ONE, 8(8), e70814. (doi:10.1371/journal.pone.0070814) (PMID:23967111) (PMCID:PMC3743870)

2012

Hughes, J. et al. (2012) Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. PLoS Pathogens, 8(12), e1003081. (doi:10.1371/journal.ppat.1003081)

Murcia, P. R. et al. (2012) Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. PLoS Pathogens, 8(5), e1002730. (doi:10.1371/journal.ppat.1002730)

2011

Bass, C., Hebsgaard, M.B. and Hughes, J. (2011) Genomic resources for the brown planthopper, Nilaparvata lugens: transcriptome pyrosequencing and microarray design. Insect Science, 19(1), pp. 1-12. (doi:10.1111/j.1744-7917.2011.01440.x)

Hughes, J. (2011) TreeRipper web application: towards a fully automated optical tree recognition software. BMC Bioinformatics, 12(1), p. 178. (doi:10.1186/1471-2105-12-178)

2010

Hammer, S., Brown, R., Bugoni, L., Palma, R.L. and Hughes, J. (2010) On the origin of Halipeurus heraldicus on Round Island petrels: cophylogenetic relationships between petrels and their chewing lice. Molecular Phylogenetics and Evolution, 55(3), pp. 1111-1120. (doi:10.1016/j.ympev.2010.01.013)

2007

Hughes, J. and Page, R.D.M. (2007) Comparative tests of ectoparasite species richness in seabirds. BMC Evolutionary Biology, 7(227), pp. 1-21. (doi:10.1186/1471-2148-7-227)

This list was generated on Sat Oct 19 00:23:19 2019 BST.
Jump to: Articles
Number of items: 49.

Articles

Modha, S. , Hughes, J. , Bianco, G., Ferguson, H. M. , Helm, B., Tong, L., Wilkie, G. S., Kohl, A. and Schnettler, E. (2019) Metaviromics reveals unknown viral diversity in the biting midge Culicoides impunctatus. Viruses, 11(9), 865. (doi:10.3390/v11090865)

Suárez, N. M. et al. (2019) Human cytomegalovirus genomes sequenced directly from clinical material: variation, multiple-strain infection, recombination and gene loss. Journal of Infectious Diseases, 220(5), pp. 781-791. (PMID:31050742) (PMCID:PMC6667795)

Rihn, S. J. et al. (2019) TRIM69 inhibits Vesicular Stomatitis Indiana Virus (VSIV). Journal of Virology, (Accepted for Publication)

Alamil, M., Hughes, J. , Berthier, K., Desbiez, C., Thébaud, G. and Soubeyrand, S. (2019) Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1775), 20180258. (PMID:31056055)

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)

Davis, C. et al. (2019) New highly diverse hepatitis C strains detected in sub‐Saharan Africa have unknown susceptibility to direct‐acting antiviral treatments. Hepatology, 69(4), pp. 1426-1441. (doi:10.1002/hep.30342) (PMID:30387174) (PMCID:PMC6492010)

Rezelj, V. V., Mottram, T. J., Hughes, J. , Elliott, R. M., Kohl, A. and Brennan, B. (2019) M segment-based minigenomes and virus-like particle assays as an approach to assess the potential of tick-borne Phlebovirus genome reassortment. Journal of Virology, 93(6), e02068-18. (doi:10.1128/JVI.02068-18) (PMID:30567991) (PMCID:PMC6401446)

Zhu, H. et al. (2019) Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds. PLoS Pathogens, 15(2), e1007531. (doi:10.1371/journal.ppat.1007531) (PMID:30731004) (PMCID:PMC6366691)

Maabar, M., Davison, A. J. , Vučak, M., Thorburn, F., Gunson, R., Palmarini, M. and Hughes, J. (2019) DisCVR: rapid viral diagnosis from high-throughput sequencing data. Virus Evolution, (Accepted for Publication)

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)

Mercuri, L., Thomson, E. C. , Hughes, J. and Karayiannis, P. (2018) Quasispecies changes with distinctive point mutations in the Hepatitis C virus internal ribosome entry site (IRES) derived from PBMCs and plasma. Advances in Virology, 2018, 4835252. (doi:10.1155/2018/4835252) (PMID:30581467) (PMCID:PMC6276526)

Dunlop, J. I. et al. (2018) Development of reverse genetics systems and investigation of host response antagonism and reassortment potential for Cache Valley and Kairi viruses, two emerging orthobunyaviruses of the Americas. PLoS Neglected Tropical Diseases, 12(10), e0006884. (doi:10.1371/journal.pntd.0006884) (PMID:30372452) (PMCID:PMC6245839)

Modha, S. , Thanki, A., Cotmore, S. F., Davison, A. J. and Hughes, J. (2018) ViCTree: an automated framework for taxonomic classification from protein sequences. Bioinformatics, 34(13), pp. 2195-2200. (doi:10.1093/bioinformatics/bty099) (PMID:29474519) (PMCID:PMC6022645)

Saucedo, B. et al. (2018) Ranavirus genotypes in the Netherlands and their potential association with virulence in water frogs (Pelophylax spp.). Emerging Microbes and Infections, 7(1), 56. (doi:10.1038/s41426-018-0058-5) (PMID:29615625) (PMCID:PMC5882854)

da Silva Filipe, A. et al. (2018) Reply to: "Reply to: 'Response to DAA therapy in the NHS England Early Access Programme for rare HCV subtypes from low and middle income countries'". Journal of Hepatology, 68(4), pp. 864-866. (doi:10.1016/j.jhep.2017.11.044) (PMID:29339112)

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)

da Silva Filipe, A. et al. (2017) Response to DAA therapy in the NHS England early access programme for rare HCV subtypes from low and middle income countries. Journal of Hepatology, 67(6), pp. 1348-1350. (doi:10.1016/j.jhep.2017.06.035) (PMID:28789880)

Saucedo, B., Hughes, J. , van Beurden, S. J., Suárez, N. M., Haenen, O. L.M., Voorbergen-Laarman, M., Gröne, A. and Kik, M. J.L. (2017) Complete genome sequence of Frog virus 3, isolated from a strawberry poison frog (Oophaga pumilio) imported from Nicaragua into the Netherlands. Genome Announcements, 5(35), e00863-17. (doi:10.1128/genomeA.00863-17) (PMID:28860243) (PMCID:PMC5578841)

Milani, A. et al. (2017) Vaccine immune pressure influences viral population complexity of avian influenza virus during infection. Veterinary Microbiology, 203, pp. 88-94. (doi:10.1016/j.vetmic.2017.02.016)

Rihn, S. J. , Foster, T. L., Busnadiego, I., Aziz, M. A., Hughes, J. , Neil, S. J.D. and Wilson, S. J. (2017) The envelope gene of transmitted HIV-1 resists a late interferon gamma-induced block. Journal of Virology, 91(7), e02254-16. (doi:10.1128/JVI.02254-16) (PMID:28100611) (PMCID:PMC5355616)

Donald, C. L. et al. (2016) Full genome sequence and sfRNA interferon antagonist activity of Zika virus from Recife, Brazil. PLoS Neglected Tropical Diseases, 10(10), e0005048. (doi:10.1371/journal.pntd.0005048) (PMID:27706161) (PMCID:PMC5051680)

Franzo, G., Cortey, M., Segalés, J., Hughes, J. and Drigo, M. (2016) Phylodynamic analysis of porcine circovirus type 2: Methodological approach and datasets. Data In Brief, 8, pp. 549-552. (doi:10.1016/j.dib.2016.06.005) (PMID:27508215) (PMCID:PMC4962815)

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)

Franzo, G., Cortey, M., Segalés, J., Hughes, J. and Drigo, M. (2016) Phylodynamic analysis of porcine circovirus type 2 reveals global waves of emerging genotypes and the circulation of recombinant forms. Molecular Phylogenetics and Evolution, 100, pp. 269-280. (doi:10.1016/j.ympev.2016.04.028) (PMID:27114187)

Fusaro, A. et al. (2016) Unexpected interfarm transmission dynamics during a highly pathogenic avian influenza epidemic. Journal of Virology, 90(14), pp. 6401-6411. (doi:10.1128/jvi.00538-16) (PMID:27147741) (PMCID:PMC4936132)

Robinson, M. W., Hughes, J. , Wilkie, G. S., Swann, R. , Barclay, S. T., Mills, P. R., Patel, A. H. , Thomson, E. C. and McLauchlan, J. (2016) Tracking TCRß sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region. Frontiers in Immunology, 7, 131. (doi:10.3389/fimmu.2016.00131) (PMID:27092143) (PMCID:PMC4820669)

Orton, R.J. , Gu, Q., Hughes, J. , Maabar, M., Modha, S. , Vattipally, S. , Wilkie, G.S. and Davison, A. (2016) Bioinformatics tools for analysing viral genomic data. Revue scientifique et technique (International Office of Epizootics), 35(1), pp. 241-285. (doi:10.20506/rst.35.1.2432) (PMID:27217183)

Rijks, J. M. et al. (2016) Investigation of amphibian mortality events in wildlife reveals an on-going ranavirus epidemic in the North of the Netherlands. PLoS ONE, 11(6), e0157473. (doi:10.1371/journal.pone.0157473) (PMID:27315226) (PMCID:PMC4912076)

Stewart, M. et al. (2015) Characterization of a second open reading frame in genome segment 10 of bluetongue virus. Journal of General Virology, 96(11), pp. 3280-3293. (doi:10.1099/jgv.0.000267) (PMID:26290332) (PMCID:PMC4806581)

Nomikou, K., Hughes, J. , Wash, R., Kellam, P., Breard, E., Zientara, S., Palmarini, M. , Biek, R. and Mertens, P. (2015) Widespread reassortment shapes the evolution and epidemiology of bluetongue virus following European invasion. PLoS Pathogens, 11(8), e1005056. (doi:10.1371/journal.ppat.1005056) (PMID:26252219) (PMCID:PMC4529188)

Tilston-Lunel, N. L., Hughes, J. , Olszanski Acrani, G., da Silva, D. E.A., Azevedo, R. S.S., Rodrigues, S. G., Vasconcelos, P. F.C., Nunes, M. R.T. and Elliott, R. M. (2015) Genetic analysis of members of the species Oropouche virus and identification of a novel M segment sequence. Journal of General Virology, 96(7), pp. 1636-1650. (doi:10.1099/vir.0.000108) (PMID:25735305) (PMCID:PMC4635451)

Abdelrahman, T., Hughes, J. , Main, J., McLauchlan, J. , Thursz, M. and Thomson, E. (2015) Reply. Hepatology, 61(4), p. 1438. (doi:10.1002/hep.27393) (PMID:25147121) (PMCID:PMC4407921)

Ardelrahman, T., Hughes, J. , Main, J., McLauchlan, J. , Thursz, M. and Thomson, E. (2015) Waiting time and transplantation for hepatocellular cancer: a balance between tempus fugit and carpe diem. Hepatology, 61(4), pp. 1438-1439. (doi:10.1002/hep.27434)

Beczkowski, P. M., Hughes, J. , Biek, R. , Litster, A., Willett, B. J. and Hosie, M. J. (2015) Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus (FIV). Journal of General Virology, 96(4), pp. 893-903. (doi:10.1099/vir.0.000035) (PMID:25535323) (PMCID:PMC4361796)

Abdelrahman, T., Hughes, J. , Main, J., McLauchlan, J. , Thursz, M. and Thomson, E. (2015) Next generation sequencing sheds light on the natural history of hepatitis C infection in patients that fail treatment. Hepatology, 61(1), pp. 88-97. (doi:10.1002/hep.27192) (PMID:24797101) (PMCID:PMC4303934)

Rihn, S. J. , Hughes, J. , Wilson, S. J. and Bieniasz, P. D. (2015) Uneven genetic robustness of HIV-1 integrase. Journal of Virology, 89(1), pp. 552-567. (doi:10.1128/JVI.02451-14)

Fusaro, A., Tassoni, L., Hughes, J. , Milani, A., Salviato, A., Schivo, A., Murcia, P. R. , Bonfanti, L., Cattoli, G. and Monne, I. (2015) Evolutionary trajectories of two distinct avian influenza epidemics: parallelisms and divergences. Infection, Genetics and Evolution, 34, pp. 457-466. (doi:10.1016/j.meegid.2015.05.020) (PMID:26003682)

Zhu, H., Hughes, J. and Murcia, P. R. (2015) Origins and evolutionary dynamics of H3N2 canine influenza virus. Journal of Virology, 89(10), pp. 5406-5418. (doi:10.1128/JVI.03395-14)

Bęczkowski, P. M., Hughes, J. , Biek, R. , Litster, A., Willett, B. J. and Hosie, M. J. (2014) Feline immunodeficiency virus (FIV) env recombinants are common in natural infections. Retrovirology, 11(80), (doi:10.1186/s12977-014-0080-1) (PMID:25699660) (PMCID:PMC4180853)

Busnadiego, I. et al. (2014) Host and viral determinants of Mx2 antiretroviral activity. Journal of Virology, 88(14), pp. 7738-7752. (doi:10.1128/JVI.00214-14) (PMID:24760893) (PMCID:PMC4097781)

Jombart, T. et al. (2014) OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics, 7, pp. 28-34. (doi:10.1016/j.epidem.2014.04.003)

Monne, I. et al. (2014) Emergence of a highly pathogenic avian influenza virus from a low-pathogenic progenitor. Journal of Virology, 88(8), pp. 4375-4388. (doi:10.1128/JVI.03181-13)

Varela, M. et al. (2013) Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in Rhesus Macaques. PLoS ONE, 8(8), e70814. (doi:10.1371/journal.pone.0070814) (PMID:23967111) (PMCID:PMC3743870)

Hughes, J. et al. (2012) Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks. PLoS Pathogens, 8(12), e1003081. (doi:10.1371/journal.ppat.1003081)

Murcia, P. R. et al. (2012) Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs. PLoS Pathogens, 8(5), e1002730. (doi:10.1371/journal.ppat.1002730)

Bass, C., Hebsgaard, M.B. and Hughes, J. (2011) Genomic resources for the brown planthopper, Nilaparvata lugens: transcriptome pyrosequencing and microarray design. Insect Science, 19(1), pp. 1-12. (doi:10.1111/j.1744-7917.2011.01440.x)

Hughes, J. (2011) TreeRipper web application: towards a fully automated optical tree recognition software. BMC Bioinformatics, 12(1), p. 178. (doi:10.1186/1471-2105-12-178)

Hammer, S., Brown, R., Bugoni, L., Palma, R.L. and Hughes, J. (2010) On the origin of Halipeurus heraldicus on Round Island petrels: cophylogenetic relationships between petrels and their chewing lice. Molecular Phylogenetics and Evolution, 55(3), pp. 1111-1120. (doi:10.1016/j.ympev.2010.01.013)

Hughes, J. and Page, R.D.M. (2007) Comparative tests of ectoparasite species richness in seabirds. BMC Evolutionary Biology, 7(227), pp. 1-21. (doi:10.1186/1471-2148-7-227)

This list was generated on Sat Oct 19 00:23:19 2019 BST.

Grants

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

  • HIV cluster detection pipeline for WoSSVC
    NHS Greater Glasgow and Clyde Endowment Funds
    2019 - 2020
     

Research datasets

Jump to: 2019
Number of items: 1.

2019

Rezelj, V. V., Mottram, T., Hughes, J., Elliott, R. M., Kohl, A. and Brennan, B. (2019) M segment-based minigenomes and virus-like particle assays as an approach to assess the potential of tick-borne Phlebovirus genome reassortment. [Data Collection]

This list was generated on Sat Oct 19 00:20:46 2019 BST.