New preprint: predicting rifampicin resistance Philip Fowler, 16th August 202416th August 2024 In this preprint we train a series of machine learning models on protein mutations found in rpoB — this is the gene in the M. tuberculosis RNA polymerase complex where mutations can introduce resistance to rifampicin, an important first-line drug in the treatment of tuberculosis. Unlike pyrazinamide, which we have previously published and binds to pncA, the RNA polymerase is an essential gene and therefore resistance-conferring mutations tend to be subtle and, in this case, mostly close to the rifampicin binding site. We find that all the models achieve similar levels of prediction performance and that the most predictive feature is, perhaps unsurprisingly, the distance from the amino acid being mutated to the centre of mass of rifampicin. All the data and code required to create our Test+Train datasets, train the models and produce nearly all the figures in the preprint is available on GitHub. Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Related antimicrobial resistance computing publication research tuberculosis
antimicrobial resistance Genetics and Tuberculosis: A Case of New Meets Old 12th July 2019 I was very pleased to be invited to contribute to this “Voices” article organised by… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
citizen science Automated detection of bacterial growth on 96-well plates (AMyGDA) 11th December 20175th August 2018 I am involved in an international collaboration, the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
New publication: CRyPTIC GWAS of antitubercular resistance 16th August 202216th August 2022 Since the primary goal of CRyPTIC was to map the genetic variants in M. tuberculosis… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More