These pages summarise studies of the virus-host interface conducted by the Gifford Lab and our collaborators.

In these research projects, the database integrated genome screening (DIGS) tool was used to investigate the evolution of virus-interacting proteins.

GLUE Projects

A3-Evolution: an investigation into the evolution of APOBEC3G, conducted in collaboration with Kei Sato's lab.

IFNL-Evolution: [pending release 2021]

KZFP-Evolution: [pending release 2022]

Related Resources

DIGS for EVEs: Systematic screening of eukaryotic whole genome sequence (WGS) data for endogenous viral elements (EVEs).

Orthologous Clusters: This database catalogues the interferomes of 10 different species, each derived from cells in an antiviral state following stimulation with type-I interferon.

Related Publications

Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Trindade Maranhão Costa F, Freire Santana M, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Da Silva Filho JL, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Openshaw PJM, Palmarini M, Lehner PJ, Baillie JK, Rihn SJ, and SJ Wilson (2021)
A prenylated dsRNA sensor protects against severe COVID-19.
Science [view]

Ito J, Gifford RJ, and Kei Sato (2019)
Retroviruses drive the rapid evolution of mammalian APOBEC3 genes.
PNAS [view]

Singer JB, Thomson EC, McLauchlan J, Hughes J, and RJ Gifford (2018)
GLUE: A flexible software system for virus sequence data.
BMC Bioinformatics [view]

Zhu H, Dennis T, Hughes J, and RJ Gifford (2018)
Database-integrated genome screening (DIGS): exploring genomes heuristically using sequence similarity search tools and a relational database. [preprint]

Shaw AE, Hughes J, Gu Q, Behdenna A, Singer J, Dennis T, Orton RJ, Varela M, Gifford RJ, Wilson SJ and M Palmarini (2017)
Fundamental properties of the mammalian innate immune system revealed by multi-species comparison of type I interferon responses.
Plos Biology [view]


This project is licensed under the GNU Affero General Public License v. 3.0.