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: 2018 | 2017
Number of items: 5.

2018

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)

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, (doi:10.1128/JVI.00145-18) (PMID:29875243) (Early Online Publication)

Dennis, T. P.W., Souza, W. M. d., Marsile-Medun, S., Singer, J. B., Wilson, S. J. and Gifford, R. J. (2018) The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. Virus Research, (doi:10.1016/j.virusres.2018.03.014) (PMID:29601845) (Early Online Publication)

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 23 15:39:57 2018 BST.
Jump to: Articles
Number of items: 5.

Articles

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)

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, (doi:10.1128/JVI.00145-18) (PMID:29875243) (Early Online Publication)

Dennis, T. P.W., Souza, W. M. d., Marsile-Medun, S., Singer, J. B., Wilson, S. J. and Gifford, R. J. (2018) The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes. Virus Research, (doi:10.1016/j.virusres.2018.03.014) (PMID:29601845) (Early Online Publication)

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 23 15:39:57 2018 BST.