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Luis Pedro Coelho @luispedrocoelho.bsky.social · 12d

See www.biorxiv.org/content/10.1... by @annacusco.bsky.social et al

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort

Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-rea...

www.biorxiv.org

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Reposted by Luis Pedro Coelho

Anna Cusco @annacusco.bsky.social · 15d

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...

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort

Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-rea...

www.biorxiv.org

3 10 20

Luis Pedro Coelho @luispedrocoelho.bsky.social · 20d

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...

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Reposted by Luis Pedro Coelho

EMBL Events @events.embl.org · 21d

🦠🌍 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!

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Reposted by Luis Pedro Coelho

Microbiome Virtual International Forum @microbiomevif.bsky.social · Sep 3

#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

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Luis Pedro Coelho @luispedrocoelho.bsky.social · Aug 22

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...

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Reposted by Luis Pedro Coelho

European Commission @ec.europa.eu · Aug 5

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
💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰

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Reposted by Luis Pedro Coelho

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Jul 31

- 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

3 10 31

Luis Pedro Coelho @luispedrocoelho.bsky.social · Jul 23

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..

Luis Pedro Coelho @luispedrocoelho.bsky.social · Jul 23

Testing whether the social media preview is better...

ismb-schedule.luispedro.org

ISMB 2025 Schedule

Interactive schedule for the ISMB 2025 conference

ismb-schedule.luispedro.org

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Luis Pedro Coelho @luispedrocoelho.bsky.social · Jul 22

For example

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

Main

ismb-schedule.luispedro.org

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Luis Pedro Coelho @luispedrocoelho.bsky.social · Jul 22

New feature this year, share a talk link

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Luis Pedro Coelho @luispedrocoelho.bsky.social · Jul 21

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

ismb-schedule.luispedro.org

Main

ismb-schedule.luispedro.org

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Luis Pedro Coelho @luispedrocoelho.bsky.social · Jul 13

New substack

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

UK. Links. Tweets. Photo

Visiting the UK. Links. Photo

luispedro.substack.com

Reposted by Luis Pedro Coelho

abacbs.bsky.social @abacbs.bsky.social · Jul 4

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!

ABACBS 2025 Conference

Adelaide, South Australia. Nov. 24-

www.abacbs.org

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Reposted by Luis Pedro Coelho

Oleksandr Maistrenko @omaistrenko.bsky.social · Jun 30

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

Sebastian Schmidt @tsbschm.bsky.social · Jun 27

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 🧵.

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Jun 27

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

3 6 21

Reposted by Luis Pedro Coelho

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Jun 27

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

4 10

Reposted by Luis Pedro Coelho

Sebastian Schmidt @tsbschm.bsky.social · Jun 27

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 🧵.

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Jun 27

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

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Reposted by Luis Pedro Coelho

Vishnu Prasoodanan, PhD @vishnuprasoodanan.bsky.social · Jun 27

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?"

Sebastian Schmidt @tsbschm.bsky.social · Jun 27

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 🧵.

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Jun 27

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

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Reposted by Luis Pedro Coelho

Sebastian Schmidt @tsbschm.bsky.social · Jun 27

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

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Luis Pedro Coelho @luispedrocoelho.bsky.social · Jun 13

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

1

Luis Pedro Coelho @luispedrocoelho.bsky.social · Jun 13

Exactly!

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

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

Apple Research and Development Expenses 2010-2025 | AAPL

Apple annual/quarterly research and development expenses history and growth rate from 2010 to 2025. Research and development expenses can be defined as an expense arising from studies and product deve...

www.macrotrends.net

1

Reposted by Luis Pedro Coelho

Mike Boylan-Kolchin @mbkplus.bsky.social · Jun 12

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.

Carl Quintanilla @carlquintanilla.bsky.social · Jun 12

* JAPAN READIES $700M PACKAGE TO LURE TALENT AMID US BRAIN DRAIN

@reuters.com

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Reposted by Luis Pedro Coelho

Segata Lab @cibiocm.bsky.social · Jun 6

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

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Luis Pedro Coelho @luispedrocoelho.bsky.social · Jun 2

Streaming now... #ExtremelyOpenScience

www.youtube.com/watch?v=R0qB...

Extremely Open Science. Stream 2.27

YouTube video by BigDataBiology-Lab

www.youtube.com