Dr Josh Singer

  • Research Software Engineer (Centre for Virus Research)

Biography

Research software engineer with academic and commercial experience. 


Research interests

My research focuses on phylogenetic virus genome sequence databases. 

As part of the Gifford group, I have developed GLUE, a software system for virus genome sequence data. GLUE organises virus sequences within a detailed phylogenetic database. It is applicable to a wide range of virus families, and provides a rich set of computational functions. It can play a role in a range of contexts including basic research, clinical research and public health decision support. 

HCV-GLUE is a bioinformatic resource for Hepatitis C virus research, which is based on GLUE. It includes a public web version which supports automated genotyping and drug resistance analysis.


Publications

List by: Type | Date

Jump to: 2019 | 2018 | 2017
Number of items: 9.

2019

Ankcorn, M. et al. (2019) Convalescent plasma therapy for persistent hepatitis E virus infection. Journal of Hepatology, 71(2), pp. 434-438. (doi:10.1016/j.jhep.2019.04.008) (PMID:31075322)

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)

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)

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)

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)

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)

This list was generated on Tue Oct 22 20:15:46 2019 BST.
Jump to: Articles
Number of items: 9.

Articles

Ankcorn, M. et al. (2019) Convalescent plasma therapy for persistent hepatitis E virus infection. Journal of Hepatology, 71(2), pp. 434-438. (doi:10.1016/j.jhep.2019.04.008) (PMID:31075322)

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)

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)

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)

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)

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)

This list was generated on Tue Oct 22 20:15:46 2019 BST.