Luis Pedro Coelho

- 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

I had never looked up how to make this better (the default before just said "Main" in the social media preview) as I didn't think it'd be worth it, but it was the perfect task for codex..

Testing whether the social media preview is better...

ismb-schedule.luispedro.org

For example

ismb-schedule.luispedro.org?speaker=Luis...

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

UK. Links. Tweets. Photo Visiting the UK. Links. Photo

New substack

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

ABACBS 2025 Conference Adelaide, South Australia. Nov. 24-

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

Not sure what point you are trying to make. Why would that be a relevant comparison here?

If anything, revenue would be a better normalization factor and VW is not that much smaller than Apple in terms of revenue

Exactly!

If you are comparing it apples to apples, then Apple spent $30b

www.macrotrends.net/stocks/chart...

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.

EESMicrobiome

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

YouTube video by BigDataBiology-Lab Extremely Open Science. Stream 2.27

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

Extremely Open Science. Stream 2.26 YouTube video by BigDataBiology-Lab

Streaming #ExtremelyOpenScience starting now...

youtube.com/live/5cSng75...

Extremely Open Science. Stream 2.25 Extremely Open Science Stream (Season 2 Episode 25) See more information at: https://github.com/BigDataBiology/sardyne/blob/main/notes/stream-notes.md

Streaming in 15 minutes... #ExtremelyOpenScience

www.youtube.com/live/06CcRSs...

US brain drain: Nature’s guide to the initiatives drawing scientists abroad In response to US turmoil, premier establishments such as the European Research Council have launched programmes to attract talent.

In response to US turmoil, European nations and establishments have launched programmes to attract talent

https://go.nature.com/432ORoU

On Progress A bird's view on a meeting of ornithologists

New Substack: a bird's view on a meeting of ornithologists

luispedro.substack.com/p/on-progress

Thanks for the kind words and do reach out if you run into issues while using it

We like to get bugreports (because it gives us an opportunity to make things better)!

Extremely Open Science. Stream 2.24 Extremely Open Science Stream (Season 2 Episode 24) See more information at: https://github.com/BigDataBiology/sardyne/blob/main/notes/stream-notes.md

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...

Assemblies of long-read metagenomes suffer from diverse errors Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...

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 🧵

Extremely Open Science. Stream 2.23 Extremely Open Science Stream (Season 2 Episode 23) See more information at: https://github.com/BigDataBiology/sardyne/blob/main/notes/stream-notes.md

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