Skip to content
Fowler Lab
Fowler Lab

Predicting antibiotic resistance de novo

  • News
  • Research
    • Overview
    • Manifesto
    • Software
    • Reproducibility
    • Publications
  • Members
  • Teaching
  • Contact
    • PhDs
  • Wiki
Fowler Lab
Fowler Lab

Predicting antibiotic resistance de novo

Updated preprint: predicting pyrazinamide resistance

Philip Fowler, 21st November 20238th December 2023

This study was performed by Josh Carter back in 2019 and we uploaded a preprint to bioRxiv and submitted the manuscript for review. Unfortunately the reviews came back just as the UK was going into lockdown in March 2020 and my memory was that the manuscript was rejected. The editor, however, had asked for major revisions so this is a lesson for me in carefully reading one’s emails!

Josh had left the group and started a combined PhD / MD programme at Stanford University and I got involved in our Covid response work so it wasn’t until 2022 that we were able to think about this manuscript again. Fortunately, by this time the CRyPTIC Consortium had published its first dataset which allowed us to roughly double the Train/Test dataset, thereby addressing one of the reviewer’s concerns. Also another group had published a model a few months after our preprint, so we were able to benchmark the performance of our best model. Finally, the original work was done in R and we took the opportunity to rewrite everything in Python, making use of a Python package Charlotte Lynch, Dylan Adlard and myself had written (sbmlcore) to simplify adding the structural and chemical features to the different datasets.

This has enabled us to make the entire code publicly available — from parsing the original datasets to aggregating the datasets to adding the features, performing the Test/Train split, training the models and plotting all the graphs. Any interested person can therefore, we hope, reproduce our work.

To check out the updated preprint, head here, whereas the data and code can be found here.

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 group publication tuberculosis

Post navigation

Previous post
Next post

Related Posts

antimicrobial resistance

BashTheBug.net Zooniverse Citizen Science project launches today!

7th April 20175th August 2018

My citizen science project, BashTheBug, is launched today. Head over to the website or go…

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
antimicrobial resistance

BashTheBug at the Science Museum

29th March 20175th August 2018

A group of us from Modernising Medical Microbiology went to the Science Museum in London…

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: BashTheBug works!

20th May 202219th July 2022

Yesterday eLife published the first paper from our citizen science project, BashTheBug, which was launched…

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

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Privacy & Cookies: This site uses cookies. By continuing to use this website, you agree to their use.
To find out more, including how to control cookies, see here: Cookie Policy
    ©2025 Fowler Lab | WordPress Theme by SuperbThemes