Another great edition of Environmental #Metagenomics is wrapping up! Huge thanks to @oskolkov.bsky.social , @aroneys.bsky.social and all the amazing participants who joined us this week. 🙌 We wish you all the best with your research projects!

Finally, the results of my postdoc at the @bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs. See our new preprint: www.biorxiv.org/content/10.1...

Full thread will come later, but @annacusco.bsky.social's preprint on the dog pet gut microbiome is out! Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases doi.org/10.1101/2025...

🦠🌍 Welcome to Day 2 of #EESMicrobiome We’re kicking things off with Session 2: Functional insights into microbial communities 🧬 🔹 First talk: “Small proteins of the human microbiome and beyond” by Luis Pedro Coelho – Queensland University of Technology Stay tuned for more exciting science!

#MeetTheSpeakers #GloMiNe2025 Atlantic event closing talks: Viral diversity in the human microbiome by Curtis Huttenhower (@hutlab.bsky.social)‬ and Cataloging the global microbiome. Very big data for very small things by @luispedrocoelho.bsky.social (@bigdatabiology.bsky.social)‬ 9/n

This is a major issue is that the incentives are to output false positives in your tools If you need to survive on having many citations to your tools, it is better if your tool gives users lots of results so that they cite it! open.substack.com/pub/luispedr...

Double the discovery, double the momentum 🚀 Europe doubles down on research competitiveness with a major boost to #HorizonEurope: €95.5 billion foreseen for 2021-2027 💰💰💰💰💰💰💰💰💰 €175 billion proposed for 2028-2034 💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰

- Model bacterial genomes as sequences of proteins - predict protein-protein interactions, operon structure, and protein function - infer phenotypic traits - design synthetic genomes with desired properties @macwiatrak.bsky.social @mariabrbic.bsky.social @andresfloto.bsky.social

Testing whether the social media preview is better... ismb-schedule.luispedro.org

New feature this year, share a talk link

After a few people asked me about it, I gave in and updated my light ISMB schedule website for #ISMBECCB2025 ismb-schedule.luispedro.org

New substack luispedro.substack.com/p/uk-links-t...

The day is finally here! 🎉 We’re releasing the invited speaker line-up, key dates, and lots more info for ABACBS 2025. Check it out and share widely: www.abacbs.org/abacbs2025 Registrations and abstract submissions open next week, with abstracts due in August!

Our preprint on estimating how many more prokaryotic taxa can be discovered in the unbinned fraction of metagenomic samples. We predict that there are 10 archaeal and 145 bacterial novel phyla across all habitats. #MicrobialDarkMatter #TreeOfLife #Microbiome #Archaea #Bacteria #Metagenomics

A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1

The team's first preprint is out! Led by ‪ ‪@vishnuprasoodanan.bsky.social‬‬ & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data? A 🧵.

New Preprint Alert! 🌍🧬 We’re thrilled to share our latest study tackling one of the biggest question.. "How many prokaryotic species, genera, and deeper lineages actually exist on Earth?"

Finally, thanks to all other co-authors: A Fullam, @ecekartal.bsky.social‬ , @pangenomics.bsky.social , @luispedrocoelho.bsky.social , A Spang & @borklab.bsky.social And of course to the lead authors @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social

The combined 2024 budgets of NSF, NIH, and NASA were around $80 billion, or 100x this package. It makes sense for other countries to try to capitalize on the idiocy that has captured our government, but it's important to remember the sheer scale and irreplaceability of the US research enterprise.

Join us at #EESMicrobiome! Organisers Mani Arumugam (#uni_copenhagen), Ami Bhatt (@stanfordpress.bsky.social), Peer Bork (@borklab.bsky.social) and Nicola Segata (#CIBIO_UniTrento) look forward to welcoming #microbiome scientists in September at @embl.org! @events.embl.org

Streaming now... #ExtremelyOpenScience www.youtube.com/watch?v=R0qB...

This week at the Hebrew U. Microbiology Journal Club: Luis Pedro Coelho, Queensland University of Technology @luispedrocoelho.bsky.social presenting on "Big data and small genes", June 5th 9am Israel time. You're welcome. Link below:

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

Streaming #ExtremelyOpenScience starting now... youtube.com/live/5cSng75...

Streaming in 15 minutes... #ExtremelyOpenScience www.youtube.com/live/06CcRSs...

In response to US turmoil, European nations and establishments have launched programmes to attract talent https://go.nature.com/432ORoU

New Substack: a bird's view on a meeting of ornithologists luispedro.substack.com/p/on-progress

Streaming #ExtremelyOpenScience in ~3 minutes... youtube.com/live/HkdUe69...

Europe’s choice is clear. To put science at the heart of its economy. To become the home of scientific freedom and collaboration. And to welcome talent from all over the world. I’m glad to present the first elements of our Choose Europe Initiative. → europa.eu/!TTbWbJ

The Gulbenkian Institute of Molecular Medicine (GIMM) is one of the best research institutes in Portugal. It's currently recruiting for three Group Leaders (junior or senior) across different areas, including systems biology and bioinformatics. gimm.pt/jobs/open-ca...

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, www.biorxiv.org/content/10.1... and tell you just a little bit about it in the following 🧵

#ExtremelyOpenScience. Streaming ... (a bit late today, but didn't want to miss it after a holiday break) www.youtube.com/live/lfzWs5h...

New substack: Second generation literalism luispedro.substack.com/p/second-gen...

What would actually be a reasonable country to hold an international scientific conference in when it comes to having reasonable visa processes for most of the world? Neither the US nor EU really seem like good options nowadays

I’m sorry but if your students use AI to write papers and you use AI to grade them zero school is happening. You are running together on a hamster wheel

ArgNorm 0.8.0 released! More information including English language names for outputs and a bugfix for handling abricate+resfinder outputs argnorm.readthedocs.io/en/latest/wh...

I'm planning to attend #ISMBECCB2025 in Liverpool in July and will spend a few days in London beforehand (July 16-19). If you are around then, let's get coffee? Or invite me to visit your institution?

Getting ready to stream #ExtremelyOpenScience... youtube.com/live/Q6Tegem...

New substack, a review of a book borrowed from the Library of Babel A cultural theory of industrial organization luispedro.substack.com/p/book-revie...

Dominant taxa in microbiomes are obviously important but here's a discussion on low abundance taxa that are highly persisting/prevalent. We can see a lot of these in metagenomics, often obscured by a high false negative rate. 🔗 www.sciencedirect.com/science/arti...

Omg Alex Chan is smashing it talking about building things to last. "Will an open source piece of code be supported 20 years into the future". Manual legal processes to approve every node dependency? Good luck with that. #monkigras how do you know what's built to last?

Small proteins can be more complex than they look! We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!

Streaming in 20 minutes... #ExtremelyOpenScience www.youtube.com/live/bIDUaq2...

Interested in doing a sabbatical at EMBL, at one of its 6 sites in Barcelona, Cambridge, Grenoble, Hamburg, Heidelberg or Rome? Funding call with deadline 15 June, decisions in July. www.embl.org/about/info/s...

SemiBin v2.2.0 released! This includes a lot of minor fixes rather than any big new features Generally speaking, SemiBin v2.2.0 is more robust, will fail in fewer corner cases and will give you better error messages when it does. semibin.readthedocs.io/en/latest/wh...

Streaming in ~4 minutes... #ExtremelyOpenScience www.youtube.com/watch?v=5w0D...

We are looking for PhD students! Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome

AI Machine Learning could potentially unblock the antimicrobial drug development pipeline and help us find the antibiotic needle in the haystack. amr-action.au/ai-a-potenti... @luispedrocoelho.bsky.social @monashuniversity.bsky.social #minimisingAMR #AMR #antimicrobialresistance #AI

ArgNorm version 0.7.0 released! A lot of improvements, including an update to CARD v4, support for AMRFinderPlus 4, an updated manual curation for many genes argnorm.readthedocs.io/en/latest/wh...