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: Share on X (Opens in new window) X Share on Bluesky (Opens in new window) Bluesky Email a link to a friend (Opens in new window) Email Share on LinkedIn (Opens in new window) LinkedIn Share on Mastodon (Opens in new window) Mastodon Related antimicrobial resistance computing publication research tuberculosis
antimicrobial resistance New paper: predicting rifampicin resistance via free energy simulation 23rd September 20253rd October 2025 This work was carried out by Xibei Zhang, who is doing her PhD with Peter… Share this: Share on X (Opens in new window) X Share on Bluesky (Opens in new window) Bluesky Email a link to a friend (Opens in new window) Email Share on LinkedIn (Opens in new window) LinkedIn Share on Mastodon (Opens in new window) Mastodon Read More
antimicrobial resistance New paper: automatically and reproducibly building a catalogue bedaquline resistance-associated variants 18th June 20251st July 2025 Dylan Adlard‘s paper describing how we can rapidly automatically build catalogues of bedaquiline resistance-associated variants… Share this: Share on X (Opens in new window) X Share on Bluesky (Opens in new window) Bluesky Email a link to a friend (Opens in new window) Email Share on LinkedIn (Opens in new window) LinkedIn Share on Mastodon (Opens in new window) Mastodon Read More
New preprint: evaluating a laboratory workflow for sequencing Mycobacteria using long-read sequencing 7th February 20269th April 2026 In this preprint, we describe and evaluate a laboratory workflow for sequencing Mycobacterial samples using… Share this: Share on X (Opens in new window) X Share on Bluesky (Opens in new window) Bluesky Email a link to a friend (Opens in new window) Email Share on LinkedIn (Opens in new window) LinkedIn Share on Mastodon (Opens in new window) Mastodon Read More