Interested in modelling metabolism from food -> gut microbiome -> blood ? 5 days left to apply for a fully funded position to investigate this. 👇👇👇

New blog post!

metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...

Both tools improved considerably! Time to update your conda environments 😄

If you are UK-based and working on any aspect of microbiomes (human, plant, insect, soil, animal, ...), please do sign up to Microbiome-Net for details of networking, funding and training opportunities.

forms.office.com/pages/respon...

Come be our head of bioinformatics at @mrc-lms.bsky.social !

Our bioinformatics team are closely involved with lots of interesting science and we love working with them. Topics inc. development, cancer, metabolism, aging, TEs (my favourite of course 😜) #TEsky lms.mrc.ac.uk/work/vacanci...

Lib Dems: We have 12x Reform's MPs, can we have the same coverage?

BBC: But Reform has 2x your poll rating. If there were an election tomorrow, they'd be running the country.

Lib Dems: So you're putting their people and policies under scrutiny, right?

BBC:

Lib Dems: Right?

"In a landmark study, OpenAI researchers reveal that large language models will always produce plausible but false outputs, even with perfect data, due to fundamental statistical and computational limits."

www.computerworld.com/article/4059...

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky

We want to explore the metabolic interactions among gut bacteria, when the human host eats different foods - maybe this explain partly the Enterosignature structure?
Please do apply for our bioinformatic post to explore this question in metagenomes: jobs.quadram.ac.uk/Details.asp?...

The AI hype is so wild that we know see charts like this and think that "must have made by AI".
Or are marketing teams worse than AI nowadays?

Yes. Check this out youtu.be/0xS68sl2D70?...

🧪 Just out in Bioinformatics Advances: “Structure-based metabolite function prediction using graph neural networks”   

Explore the full study here: https://doi.org/10.1093/bioadv/vbaf174

Authors include: @alisaadatv.bsky.social, @jannahastings.bsky.social

The right-wing press is going mad over votes at 16 ("a naked attempt to twist democracy in Labour’s favour", an "election-rigging move"...)

Oddly, they said the same 100 years ago when the voting age for women fell from 30 to 21.

Let's revisit the Mail's campaign to"Stop the Flapper Vote Folly"...

Happy Independence Day ⭐️

happy Transposon Day @yaasircheema.bsky.social and co :)

🆕 Blog! We hear from some of our researchers about their experience of attending the #Biofilms11 conference which brought together experts in biofilms 🦠

➡️ buff.ly/rgQkywB

@dr-bilal-djeghout.bsky.social @jcihorton.bsky.social ‬ @hoyuliu.bsky.sociall

⏰ Closing soon! We’re looking for a Senior Bioinformatics Engineer to join the Core Bioinformatics team and define the bioinformatics support behind the institute’s research into gut health, microbiology and food 🧬

💷 £44,500 to £55,000
🗓️ Apply by 19 May 2025
➡️ buff.ly/qcolF3D

😢

DeSciDe: A tool for unbiased literature searching and gene list cu-ration unveils a new role for the acidic patch mutation H2A E92K https://www.biorxiv.org/content/10.1101/2025.05.05.652253v1

…

Interesting: MIT's Boltz-1 is a fully open-source model for predicting complex protein structures.
Unlike AlphaFold, which gives a single "best guess," MIT's Boltz-1 models the probability of different possible protein structures, capturing their natural flexibility.

news.mit.edu/2024/researc...

Check out Wu et al.'s paper on MetaX, a peptide-centric platform. High-resolution insights into “who is doing what and how” in microbial ecosystems.
⚡️ Outperforms protein-centric tools
🔍 Reveals taxa-function links at peptide level. i.e. Deep dive in taxa-function
pubs.acs.org/doi/10.1021/...

I got hit by some rather sudden and extreme financial hardship so if anyone is in need of remote wetlab contract research, strictly BSL1, do let me know. Currently scrambling for gigs.

Plant, Bacterial, Archaeal Non-model Bioeng
Custom Lab Hardware
Turn Key Genetic Design

Please repost for reach 💚

Small update from AllTheBacteria (allthebacteria.org). Assemblies can be bulk downloaded from OSF as before, or you can now get individual assemblies from AWS. We now also have a LexicMap index on AWS, so you can align your favourite gene against 2.4million bacteria (next post for price estimates)

AFESM: a metagenomic guide through the protein structure universe! We clustered 821M structures (AFDB&ESMatlas) into 5.12M groups; revealing biome-specific groups, only 1 new fold even after AlphaFold2 re-prediction & many novel domain combos. 🧵
🌐 afesm.foldseek.com
📄 www.biorxiv.org/content/10.1...