Imperial College London


Faculty of MedicineSchool of Public Health

Honorary Research Associate







VC9Medical SchoolSt Mary's Campus





As of January 2017, I have moved to the Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, and am no longer directly affiliated with Imperial College (although the Cryptococcal project described below continues - see Prof Matthew Fisher, matthew.fisher[at]  

For academic queries, I can be contacted at mathew.beale[at]

Imperial Bio (2012-2015):

I am a molecular biologist, microbiologist, and bioinformatician.  My main research interests are in the relationships between microbial genotype and the clinical phenotype caused by pathogenic microorganisms, and in the emergence of drug resistance.  I develop and apply molecular techniques such as whole genome sequencing and RNA-Seq to study different populations of microorganisms to try and understand how they differ at the molecular level.  The hope is that these findings will lead to a better understanding of disease pathology and to better drug targets for treatment. 

In my current role, based jointly in the Fisher Group at Imperial and the Bicanic Group at St George's University London, my primary focus is on the yeast Cryptococcus neoformans, an opportunistic fungal infection of HIV infected individuals that is responsible for up to 800,000 annual deaths in Africa.  I recently whole genome sequenced ~300 isolates from a variety of Clinical patients as well as from Environmental sources, and we are currently analysing this data using population genomics techniques under a GWAS framework.  I am also developing methods for transcriptional profiling of Cryptococcus under different physiological and environmental conditions, as well as developing other novel methods for genomic analysis, and supporting other genomics projects within the group. 



Hamilton WL, Tonkin-Hill G, Smith ER, et al., 2021, Genomic epidemiology of COVID-19 in care homes in the east of England., Elife, Vol:10

Rodrigues AM, Beale MA, Hagen F, et al., 2020, The global epidemiology of emerging Histoplasma species in recent years, Studies in Mycology, Vol:97, ISSN:0166-0616

Aanensen DM, Abudahab K, Adams A, et al., 2020, An integrated national scale SARS-CoV-2 genomic surveillance network, The Lancet Microbe, Vol:1, ISSN:2666-5247, Pages:E99-E100

Beale MA, Noguera-Julian M, Godornes C, et al., 2020, A genomic epidemiology investigation of yaws re-emergence and bacterial drug resistance selection

Lassalle F, Beale MA, Bharucha T, et al., 2020, Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses, Virus Evolution, Vol:6, ISSN:2057-1577, Pages:1-14

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