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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 […]

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antimicrobial resistance clinical microbiology computing distributed computing grants

GPAS

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 […]

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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¬†Sonnenkalb, who is studying for her […]

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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 […]

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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 […]

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teaching

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 […]

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teaching

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 […]

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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 […]

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teaching

Adventures in online lecturing mathematics to biochemists. Part 1.

After one year of shadowing Professor Elspeth Garman, I’ve taken over lecturing the Mathematics course to the first-year undergraduates studying Biochemistry at the University of Oxford. A little over ten years ago I was a class tutor on this course and always liked it, partly because it is a challenge: I think many of the […]

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antimicrobial resistance computing distributed computing GPUs molecular dynamics publication research

New publication: how quickly can be calculate the effect of a mutation on an antibiotic?

The idea for this paper arose during talking over coffee at the BioExcel Alchemical Free Energy workshop in May 2019. We’d previously shown that alchemical free energy methods could successfully predict which mutations in S. aureus DHFR¬† confer resistance to trimethoprim (and crucially, which do not). That is all well and good, but to do […]