Members

Dylan joined the group in October 2020 and developed machine-learning models that used structural and chemical information to predict resistance to a first-line anti-TB compound.

He is currently studying for his DPhil as part of the SABS R³ programme having completed a 12 week rotation starting in April 2022 and then returning to start his DPhil project in October 2022.

I am in my second-year of the Oxford Interdisciplinary Bioscience DTP and am using the large dataset of M. tuberculosis genomes collected by CRyPTIC to identify putative mutations in the RNA polymerase that compensate for the fitness cost introduced by mutations that confer resistance to rifampicin.

I am a first year DPhil student on the IBM Computational Discovery programme, co-supervised by Philip Fowler and Joseph Morrone from IBM. My research involves using machine learning, in particular graph neural networks, to predict whether novel protein mutations can confer antibiotic resistance. Prior to starting my DPhil, I worked in data engineering at AstraZeneca, and did my undergraduate degree in Biochemistry also at Oxford.

I am an Associate Professor working in the Modernising Medical Microbiology group which is part of Experimental Medicine in the Nuffield Department of Medicine at the University of Oxford. I’m based at the John Radcliffe Hospital in Oxford, having moved here in March 2016 from the Department of Biochemistry. For more information, click the links in the menu above or check out my departmental webpages.

I joined the MMM team at the start of October as a postdoc with Philip Fowler to work on AMR prediction using machine learning. Before this I was a postdoc in the Biochemistry Department, working on biomolecular simulations of ion channels and nanopores. Both my undergraduate and DPhil degrees were in Materials Science, also at Oxford, so whilst I haven’t yet moved university, I have quite a varied background!

I am studying for a DPhil in Clinical Medicine, supervised by Philip Fowler and Sarah Walker, with funding from the Nuffield Department of Medicine. I previously undertook both Masters and undergraduate degrees in Biochemistry at the university of York. My interests are in protein structure and antibiotic resistance in M. tuberculosis.

My name is Matty and I’m studying the Part II of my MBiochem at the University of Oxford under the supervision of Philip Fowler. During my time here, I will be developing Machine Learning models to predict unknown mutations which confer resistance to TB antibiotics, specifically focusing on Isoniazid. Outside of the lab, I’m a swimmer for the university and a big Liverpool fan!

Oliver did his first rotation in the group from Jan-Mar 2017 as part of his Interdisciplinary Biosciences DTP DPhil before working in Simon Newstead’s group in Biochemistry learning structural biology techniques. He was supervised by myself and Simon and passed his DPhil viva in August 2021. His thesis is entitled Structural & Biophysical Characterisation of M. tuberculosis MmpL3.

Alexander studied for his Part II research project Oct 2019-May 2020 and studied how various mutations in Penicillin Binding Proteins from Neisseria gonorrhoeae confer resistance to beta-lactam antibiotics. He collaborated with Professor Chris Dowson’s group at Warwick University.

Josh was a Rhodes Scholar who I supervised, along with Derrick Crook, for his Masters degree that he successfully defended in June 2019. He applied different machine-learning approaches to predicting the effect of single nucleotide polymorphisms in the pncA gene on the action of pyrazinamide, one of the four first-line anti-tubercular compounds. A paper is under review and you can read the preprint here.

Dom did his research project for his Biochemistry undergraduate degree in the group between September 2018 and March 2019 and worked on determining how the free energy of binding of isoniazid to its target, KatG, is influenced by mutations in M. tuberculosis, using molecular dynamics simulations. He is now studying for a PhD at UCL in the group of Francesco Gervasio.

Mark did his fourth year (Part II) research project for his biochemistry undergraduate degree jointly in my group and Simon Newstead’s in Biochemistry working on solving the structures of several M.tuberculosis proteins.

Firdaus studied for his DPhil, Improving Oral Drug Delivery: Computational Studies of Proton Dependent Oligopeptide Transporters under the supervision of PWF. He published two key papers which you can read about here and here. He worked with Prof Syma Khalid at Southampton University for a few years and is now in the lab of Dr Peter Bond at the A*STAR Bioinformatics Institute in Singapore.