New paper: Quantitative drug susceptibility testing for M. tuberculosis using unassembled sequencing data and machine learning Philip Fowler, 14th August 202414th August 2024 This is the last paper from the initial set of CRyPTIC publications following the project’s data freeze in April 2020. The consortium takes a difference approach to that of (i) mapping the reads, (ii) look up the genetic mutations in a catalogue and (iii) return the predictions and instead trained a tree-based extreme gradient-boosted machine learning model. Since the minimum inhibitory concentration (MIC) was the label, the appropriate metrics are exact and essential agreement which mean “get the same MIC” and “get within one doubling dilution of the MIC”. The essential agreement is good for some drugs like ethambutol which have moderate sensitivities using the traditional binary approach which is expected due to their MIC distribution being almost unimodal. Also the good performance of the fluoroquinolones suggests that the model is able, in part at least, to learn the presence of minor alleles / subpopulations which we have shown elsewhere to be important for this class of drugs. But seriously: one figure and three tables? All those numbers in tables aren’t exactly easy to read and what I do I put for the thumbnail? (PWF can say this as technically he is an author and therefore it is partly his responsibility and therefore fault). 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 clinical microbiology publication tuberculosis
Updated preprint: A validated cloud-based genomic platform for co-ordinated, expedient global analysis of SARS-CoV-2 genomic epidemiology 23rd January 202528th January 2025 In August 2022 seven laboratories across the world uploaded their SARS-CoV-2 genetics files for processing… 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
computing New Publication: Predicting affinities for peptide transporters 29th January 201629th September 2018 PepT1 is a nutrient transporter found in the cells that line your small intestine. It… 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 refereed preprint: BashTheBug 31st March 202231st March 2022 BashTheBug is a citizen science project hosted on the Zooniverse platform that we launched in… 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