Ben J Woodcroft

@benjwoodcroft.bsky.social

Yet another microbial bioinformatician, group leader, dad github.com/wwood https://research.qut.edu.au/cmr/team/ben-woodcroft/

Ancestral genome reconstructions get noisier the deeper in time you go. The usual response: distrust them and joke about reading entrails. Ours is to train on the noise! The result is calibrated phenotype prediction back to the LBCA deep in the Archaean. New preprint www.biorxiv.org/content/10.6...

Models trained with noisy genomes extend bacterial phenotype prediction into deep time

Predicting phenotype from genotype in extant organisms is increasingly tractable through the accumulation of genome sequences and the development of machine-learning algorithms. Here we show that mach...

biorxiv.org

Today marks 30 years since we identified the apicoplast, a relict plastid in human and animal parasites (PMID 8632819). Apicoplasts are the target of the widely used antimalarial prophylactic doxycycline, which has saved many thousands of malaria infections.

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We’re excited to announce our keynote speakers for the JAMS 15 Symposium – Brisbane 2026! 🧬✨ This year, JAMS 15 will feature an incredible lineup of researchers and leaders in microbiology, infectious diseases, and antimicrobial resistance research.

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This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...

Researchers say the Trump administration is finding new ways to punish science

Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.

npr.org

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social doi.org/10.1093/bioa... The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives. More information on globdb.org 1/5 🖥️🧬🦠

GlobDB: a comprehensive species-dereplicated microbial genome resource

AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

doi.org

SingleM v0.20.2 - ONT/PacBio input reads now supported (if somewhat inefficiently), plus improved Lyrebird database for phage profiling. Microbial fraction is now prokaryotic fraction, easier to specify input genomes.