Alice Brankin wins NDM Prize

Congratulations to Alice who last night was awarded an NDM prize for the work she’s done in the third year of her DPhil! Very well deserved – despite locating away from Oxford due to the pandemic Alice has, amongst other things, become a key member of the CRyPTIC analysis group of the past year.

antimicrobial resistance publication research tuberculosis

New Publication: Structure of MmpL3

Oliver Adams successfully elucidated the structure of the M. tuberculosis MmpL3 membrane transporter using cryo-EM and this has recently been published online in Structure. This was the main aim of his PhD studies in Simon Newstead‘s group in the Department of Biochemistry here in Oxford. It is an important protein structure since although other MmpL3 […]

antimicrobial resistance clinical microbiology computing grants research tuberculosis

Postdoctoral position advertised

Through the CompBioMed2 EU Centre of Excellence project I have funding to appoint a postdoctoral researcher to develop machine-learning models to predict whether an infection is susceptible to an antibiotic. The need for predictive methods, such as these, will grow in the coming years as more of clinical microbiology transitions to using genetics to infer […]

antimicrobial resistance clinical microbiology computing distributed computing grants


I’ve been working on this for the last few months and very happy that we can now share our plans. Through a very generous donation by ORACLE, a group of researchers led by ModMedMicro at Oxford, are developing a cloud-based clinical microbiology genetics processing service, called the Global Pathogen Analysis System (GPAS). GPAS is still […]

antimicrobial resistance clinical microbiology publication

New preprint: Deciphering bedaquiline and clofazimine resistance in tuberculosis

In this preprint we examine 14,151 clinical isolates drawn from the CRyPTIC dataset. Each isolate had its minimum inhibitory concentration (MIC) to bedaquiline and clofazimine measured and hence we were able to identify the transcription regulator Rv0678, as the current main source of elevated MICs to both these drugs. Lindsay┬áSonnenkalb, who is studying for her […]

antimicrobial resistance clinical microbiology publication research tuberculosis

New print: Epidemiological cutoff values for a 96-well broth microdilution plate for M. tuberculosis

In this preprint, the CRyPTIC project proposes the maximum value of minimum inhibitory concentration (MIC) for 13 different anti-TB drugs below which a sample can be considered to be ‘genotypically wild-type’. It is necessary to establish these values, called epidemiological cutoff values (ECOFFs or ECVs), so that the MICs measured can be converted into binary […]

antimicrobial resistance clinical microbiology computing grants research

Research position advertised

Come and work with me on antimicrobial resistance! Advert here. Broadly the idea is to develop our work using machine learning and molecular simulation to predict whether individual bacterial protein mutations confer resistance to an antibiotic (or not). Any questions please get in touch. For more details please see the advert, especially the lists of […]


Adventures in online lecturing mathematics to biochemists. Part 3.

In this post, I’ll describe the feedback I got from my students on my Quantitative Biochemistry course. It was delivered during October and November 2020 and comprised a dozen lectures and a series of seven examples classes, each led by a class tutor and containing 6-9 students. See here and here for the previous two […]


Adventures in online lecturing mathematics to biochemists. Part 2.

In the last post, I described how I’ve converted Professor Elspeth Garman’s lecture notes from OHP to jupyter-notebooks, which is quite a jump, but I had to do so I could record the dozen lectures making up the course which started in October 2020. So how did it go? Some things I learnt scribbling on […]

clinical microbiology publication

New publication: Antibody Status and Incidence of SARS-CoV-2 Infection in Health Care Workers

A second Covid-19 publication I’m proud to be (a small) part of has recently published been in the New England Journal of Medicine. Given the Oxford University Hospital’s Staff Covid testing has been running for months, as described in our first publication, the team was able to show that having antibodies led to a substantially […]