Strobealign v0.17.0 is out! github.com/ksahlin/stro...

New substack: Some links & photos Also, I'll be in Luxembourg through the end of the year and in Lisbon until the 10th of Jan. Get in touch if you want to meet up luispedro.substack.com/p/links-phot...

I have a fondness for the pronouns meaning 'with X' that you find in Spanish, Portuguese and Galician (like conmigo 'with me' and contigo 'with you'), because both the con- bit and the -go bit come from the Latin for 'with' – meaning that conmigo is etymologically 'with-me-with'.

Between these news and the astounding number of people that I know personally who had shingles even though they were "too young", I have decided to get the vaccine (and pay out of pocket) even though it is not part of the official recommendations for my age

"there's a new serif in town"

1. The European Parliament’s attempt to ban plant-based foods from being sold as “sausages”, “burgers” etc is a direct response to livestock industry lobbying. This is a short thread on how utterly bleeding ridiculous it is. 🧵1/6

IMO it’s weird and probably irresponsible to teach bioinformatics without some nod to the group dynamics that shaped (otherwise inexplicable) things like the GFF file format or the Gene Ontology. Not to mention why tools back then had names like BLAST and FASTA,but now are named after cuddly animals

We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes. Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8

New version of macrel released (v1.6.0) The biggest change is internal, using a much better approach to saving and loading models (thus removing the dependency on particular versions of scikit-learn) A few other bugfixes were included github.com/BigDataBiolo...

Celebrating Excellence at the Centre for Microbiome Research! We’re thrilled to share that Gene Tyson, @benjwoodcroft.bsky.social and @luispedrocoelho.bsky.social have once again been named Highly Cited Researchers for 2025 by Clarivate! #HighlyCited2025

Congrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published! proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes | Nucleic Acids Research | Oxford Academic https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1208/8328542?rss=1&login=true

Happy to be again named as a Highly Cited Researcher for 2025 by Clarivate! Credit to my team and collaborators who have made all of this possible and happy to also see that the Centre for Microbiome Research has 3 highly cited researchers (myself, Ben Woodcroft and Gene Tyson)! #HighlyCited2025

We've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social www.biorxiv.org/content/10.1...

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