Advanced Applications of Sequencing Technologies for Infectious Diseases resources

Nat joined the lab at the end of 2019 as a postdoctoral research fellow. Her primary research project at the Roslin Institute involves developing methods for culture-free prediction of antimicrobial resistance in canine infections, using nanopore sequencing.

Prior to joining LBEP, Nat worked for four years (2012-2016) as a bioinformatician for the International Mouse Phenotyping Consortium (IMPC), at MRC Harwell. In 2016, she moved to the University of Bath to study for a PhD. Her PhD research focussed on the use of long-read sequencing (particularly nanopore sequencing) to investigate the genome of the bacterium which causes whooping cough, Bordetella pertussis.

Nat’s main research interests are sequencing, genomics and bioinformatics. She is also a keen science communicator, having received a Postgraduate Diploma in Science Communication and Public Engagement from the University of Edinburgh in 2016.

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Sam Lycett was originally trained in physics, receiving a bachelor’s degree from the University of Cambridge and a PhD in semiconductor quantum physics from Imperial College London.

They joined the Institute of Evolutionary Biology at the University of Edinburgh as a Computational Biologist, studying influenza and HIV in Professor Andrew Leigh Brown’s group (2007–2013) and Professor Andrew Rambaut’s group (2010–2013). Since August 2024 they have been Professor of Pathogen Phylodynamics, leading research programmes in viral and bacterial evolution and epidemiology.

Their research focuses on the evolution and epidemiology of viruses and bacteria, leveraging the large and growing volume of pathogen sequence data. Because pathogen genomes accumulate mutations over time, these data can be used to infer transmission patterns. The Lycett group develops and applies advanced computational, Bayesian, machine learning, bioinformatic, and phylogenetic/phylodynamic modelling approaches to investigate cross-species transmission, host adaptation, epistatic interactions, and drivers of disease spread. Current projects span multiple pathogens, including avian influenza viruses and other fast-evolving animal and zoonotic RNA viruses, as well as DNA viruses; they also address outbreaks and epidemic spread, the effects of escape mutations, the emergence of new variants and phenotype change, and predictability within host populations.

Martin McHugh is a Principal Clinical Scientist in NHS Lothian where he leads reference laboratories for bacterial sexually transmitted infections and pathogen genomics. Martin completed his PhD at the University of St Andrews using whole genome sequencing to investigate enterococci from Scottish healthcare settings. 

Having established genomic surveillance for SARS-CoV-2 in 2020, he now applies genomic techniques to the public health surveillance of a range of infectious pathogens. Martin is an NHS Research Scotland funded Clinical Researcher with a focus on applying genomics to understand and mitigate antimicrobial resistance. 

Katerina Guschanski is a Senior Lecturer in Genomics at the University of Edinburgh. She studies how climatic and anthropogenic factors affect mammals and their associated microorganisms over long and short evolutionary timescales. By using historical and modern collections, she explores current and past biodiversity and provides a temporal perspective on the genomic responses of hosts and microorganisms to rapid environmental change. 

Her current research interest include the effects of human-made contaminants, specifically antibiotics, on host-associated microbiomes, and the interplay between hosts and microbiomes during population declines. 

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