Sir Michael Stoker Building
464 Bearsden Road
Glasgow G61 1QH

Contact Information

Call: 0141-330 4019

Email: Joseph.Hughes at

Joseph Hughes

Computational and Evolutionary biologist

MRC-University of Glasgow Centre for Virus Research

I am an evolutionary biologist with extensive experience in molecular evolution and computing.

I originally trained on aspects of insect evolution, adaptation, cospeciation and phylogenomics. Since 2011, I have been working at the CVR on a range of projects addressing virus evolution. I am especially interested in understanding the evolutionary forces shaping the solutions that viruses have found to adapt to their host and how these adaptations have resulted in the huge diversity of viruses. I also study adaptation in the host by investigating the molecular evolution of different interferon stimulated genes.

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: 

  • 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

Current projects:

  • COVID-19 Research Response through the contribution to the COG-UK Consortium and COG-UK Hospital Onset Covid-19 Infection (HOCI) Study. Processing samples for UK-level reporting by the COG-UK consortium, analysing data to inform on surveillance of SARS2 in Scotland, providing reports to Public Health Scotland with respect to local outbreaks, reporting to infection control teams on outbreaks in hospitals.
  • DARPA PREventing EMerging Pathogenic Threats (PREEMPT). Andrew, Matej and I are carrying out the genomic and bioinformatic analysis of the Mastomys herpesviruses and Lassavirus sequence data produce by Jenna as part of a large international collaboration.
  • BBSRC Genomic epidemiology of equine influenza virus in the United Kingdom. Understanding and learning from the 2019 Equine Influenza epidemics, one of the largest in the UK, to prevent and control future epidemics. 
  • DHSC/UKRI Global Effort on COVID-19 (GECO) Health Research (collaboration between IBACHM, University of Glasgow and RITM in the Philippines). Implementing genomic surveillance to support SARS-CoV-2 control and mitigation strategies in the Philippines.
  • Member of the ICTV Parvoviridae study group.

Current PhD students:

  • Rubayet Ul Alam 
  • Uladzislau Litvin
Past PhD students:
  • Spyros Lytras – Molecular signals of arms race evolution between RNA viruses and their hosts. Thesis
  • Sejal Modha – Sequence data mining and characterisation of unclassified microbial diversity. Thesis
  • Haiting Chai – Machine-learning-based identification of factors that influence molecular virus-host interactions. Thesis

Past MSc students:

  • Bowen Zheng (2023) “ViralBottleneck”: An R Package for Analysis Next Generation Sequencing Data to Measure Viral transmission bottleneck sizes. code
  • Rui Li (2023) Viral landscapes in rodent communities.
  • Sizhuo Yi (2022) Building a graph-based database for querying host-parasite sequence information. code
  • Jane Walls (2021) Benchmarking a pipeline for detecting defective interfering particles from Next Generation Sequence data. code
  • Yitian Shen (2020) Benchmarking of co-phylogenetic tools with an application to hantaviruses and their rodent hosts. code
  • Kirsty Maclean (2017) SRA Explorer: an application to visualise and explore NCBI’s Sequence Read Archive. code
  • Edward Richards (2017) 1140 rat viromes constructed via the Sequence Read Archive. code
  • Marc Niebel (2016) Diagnosing viral infections using next generation sequencing. 
  • Pengze Ma (2015) GenbankHostFilter: an automatically updated database. code