Luis Pedro Coelho
@luispedrocoelho.bsky.social
π€ 1774
π₯ 2125
π 286
Content creator for Elsevier, NPG, and others Microbiome researcher Based in Brisbane
reposted by
Luis Pedro Coelho
Physalia-courses@Online
26 days ago
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. π We wish you all the best with your research projects!
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Luis Pedro Coelho
Anna Cusco
about 2 months ago
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: π¦ microbiome, 𧬠long-reads, and πΆ dogs. See our new preprint:
www.biorxiv.org/content/10.1...
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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...
https://www.biorxiv.org/content/10.1101/2025.09.17.676595v1
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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...
about 2 months ago
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Luis Pedro Coelho
EMBL Events
about 2 months ago
π¦ π Welcome to Day 2 of
#EESMicrobiome
Weβre kicking things off with Session 2: Functional insights into microbial communities 𧬠πΉ First talk: βSmall proteins of the human microbiome and beyondβ by Luis Pedro Coelho β Queensland University of Technology Stay tuned for more exciting science!
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Luis Pedro Coelho
Microbiome Virtual International Forum
2 months ago
#MeetTheSpeakers
#GloMiNe2025
Atlantic event closing talks: Viral diversity in the human microbiome by Curtis Huttenhower (
@hutlab.bsky.social
)β¬ and Cataloging the global microbiome. Very big data for very small things by
@luispedrocoelho.bsky.social
(
@bigdatabiology.bsky.social
)β¬ 9/n
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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...
add a skeleton here at some point
3 months ago
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Luis Pedro Coelho
European Commission
3 months ago
Double the discovery, double the momentum π Europe doubles down on research competitiveness with a major boost to
#HorizonEurope
: β¬95.5 billion foreseen for 2021-2027 π°π°π°π°π°π°π°π°π° β¬175 billion proposed for 2028-2034 π°π°π°π°π°π°π°π°π°π°π°π°π°π°π°π°π°π°
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Luis Pedro Coelho
Kevin K. Yang ζ₯ε±η
3 months ago
- 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
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Testing whether the social media preview is better...
ismb-schedule.luispedro.org
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ISMB 2025 Schedule
Interactive schedule for the ISMB 2025 conference
https://ismb-schedule.luispedro.org/
4 months ago
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New feature this year, share a talk link
add a skeleton here at some point
4 months ago
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After a few people asked me about it, I gave in and updated my light ISMB schedule website for
#ISMBECCB2025
ismb-schedule.luispedro.org
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Main
https://ismb-schedule.luispedro.org/
4 months ago
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New substack
luispedro.substack.com/p/uk-links-t...
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UK. Links. Tweets. Photo
Visiting the UK. Links. Photo
https://luispedro.substack.com/p/uk-links-tweets-photo
4 months ago
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reposted by
Luis Pedro Coelho
4 months ago
The day is finally here! π Weβre 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!
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ABACBS 2025 Conference
Adelaide, South Australia. Nov. 24-
https://www.abacbs.org/abacbs2025
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Luis Pedro Coelho
Oleksandr Maistrenko
4 months ago
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
add a skeleton here at some point
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reposted by
Luis Pedro Coelho
bioRxiv Microbiology
5 months ago
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
5 months ago
The team's first preprint is out! Led by βͺ βͺ@vishnuprasoodanan.bsky.socialβ¬β¬ &
@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 π§΅.
add a skeleton here at some point
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Luis Pedro Coelho
Vishnu Prasoodanan, PhD
5 months ago
New Preprint Alert! π𧬠Weβre thrilled to share our latest study tackling one of the biggest question.. "How many prokaryotic species, genera, and deeper lineages actually exist on Earth?"
add a skeleton here at some point
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Luis Pedro Coelho
Sebastian Schmidt
5 months ago
Finally, thanks to all other co-authors: A Fullam,
@ecekartal.bsky.social
β¬ ,
@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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reposted by
Luis Pedro Coelho
Mike Boylan-Kolchin
5 months ago
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.
add a skeleton here at some point
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reposted by
Luis Pedro Coelho
Segata Lab
5 months ago
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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Streaming now...
#ExtremelyOpenScience
www.youtube.com/watch?v=R0qB...
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Extremely Open Science. Stream 2.27
YouTube video by BigDataBiology-Lab
https://www.youtube.com/watch?v=R0qBJQAm34s
5 months ago
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reposted by
Luis Pedro Coelho
Asaf Levy
5 months ago
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:
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reposted by
Luis Pedro Coelho
Jim Shaw
6 months ago
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
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myloasm - metagenomic assembly with (noisy) long reads
https://myloasm-docs.github.io/
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Streaming
#ExtremelyOpenScience
starting now...
youtube.com/live/5cSng75...
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Extremely Open Science. Stream 2.26
YouTube video by BigDataBiology-Lab
https://youtube.com/live/5cSng752PWY
6 months ago
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Streaming in 15 minutes...
#ExtremelyOpenScience
www.youtube.com/live/06CcRSs...
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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
https://www.youtube.com/live/06CcRSs_K5g
6 months ago
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reposted by
Luis Pedro Coelho
Nature
6 months ago
In response to US turmoil, European nations and establishments have launched programmes to attract talent
https://go.nature.com/432ORoU
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US brain drain: Natureβs 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.
https://go.nature.com/45eQd1b
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New Substack: a bird's view on a meeting of ornithologists
luispedro.substack.com/p/on-progress
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On Progress
A bird's view on a meeting of ornithologists
https://luispedro.substack.com/p/on-progress
6 months ago
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Streaming
#ExtremelyOpenScience
in ~3 minutes...
youtube.com/live/HkdUe69...
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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
https://youtube.com/live/HkdUe69ra3s
6 months ago
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reposted by
Luis Pedro Coelho
Ursula von der Leyen
6 months ago
Europeβs 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. Iβm glad to present the first elements of our Choose Europe Initiative. β
europa.eu/!TTbWbJ
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Luis Pedro Coelho
Pedro Beltrao
6 months ago
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...
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Research Group Leaders β GIMMResearch Group Leaders β GIMM
Thank you very much for your generous donation and for sharing your testimony.We hope to more people feel inspired to join this mission of discovery and innovation!
https://gimm.pt/jobs/open-call-research-group-leaders
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Luis Pedro Coelho
Florian Trigodet
7 months ago
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 π§΅
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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...
https://www.biorxiv.org/content/10.1101/2025.04.22.649783v2
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#ExtremelyOpenScience
. Streaming ... (a bit late today, but didn't want to miss it after a holiday break)
www.youtube.com/live/lfzWs5h...
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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
https://www.youtube.com/live/lfzWs5hIaiQ
7 months ago
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New substack: Second generation literalism
luispedro.substack.com/p/second-gen...
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Second generation literalism
What to call teal
https://luispedro.substack.com/p/second-generation-literalism
7 months ago
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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
7 months ago
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reposted by
Luis Pedro Coelho
Joseph Rezek
7 months ago
Iβm 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
add a skeleton here at some point
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reposted by
Luis Pedro Coelho
7 months ago
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...
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What's New - argNorm: Normalize ARG annotations to ARO
https://argnorm.readthedocs.io/en/latest/whatsnew/#version-080-released-on-12-april-2025
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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?
7 months ago
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Getting ready to stream
#ExtremelyOpenScience
...
youtube.com/live/Q6Tegem...
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Extremely Open Science. Stream 2.22
YouTube video by BigDataBiology-Lab
https://youtube.com/live/Q6TegemoyLU
7 months ago
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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...
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Book review: a cultural theory of industrial organisation
Borges meets ACX
https://luispedro.substack.com/p/book-review-a-cultural-theory-of
7 months ago
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reposted by
Luis Pedro Coelho
Guillaume MΓ©ric
8 months ago
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. π
www.sciencedirect.com/science/arti...
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luispedro.substack.com/p/links-twee...
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Links. Tweets. Photos (2025-W14)
Links What goes without saying
https://luispedro.substack.com/p/links-tweets-photos-2025-w14
8 months ago
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reposted by
Luis Pedro Coelho
Cake Darling Entry
8 months ago
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?
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Luis Pedro Coelho
Gabriel Rocklin
8 months ago
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!
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Streaming in 20 minutes...
#ExtremelyOpenScience
www.youtube.com/live/bIDUaq2...
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Extremely Open Science. Stream 2.21
YouTube video by BigDataBiology-Lab
https://www.youtube.com/live/bIDUaq2QpwU
8 months ago
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reposted by
Luis Pedro Coelho
Wolfgang Huber
8 months ago
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...
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Luis Pedro Coelho
8 months ago
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...
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What's New - SemiBin
https://semibin.readthedocs.io/en/latest/whatsnew/#version-220
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Streaming in ~4 minutes...
#ExtremelyOpenScience
www.youtube.com/watch?v=5w0D...
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Extremely Open Science. Stream 2.20
YouTube video by BigDataBiology-Lab
https://www.youtube.com/watch?v=5w0DdkTggmM
8 months ago
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reposted by
Luis Pedro Coelho
8 months ago
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
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Luis Pedro Coelho
Minimising AMR
8 months ago
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
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AI could be a game-changer for antibiotic drug development
AI Machine Learning could potentially unblock the antimicrobial drug development pipeline.
https://amr-action.au/ai-a-potential-game-changer-for-antibiotic-drug-development/
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Luis Pedro Coelho
8 months ago
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...
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What's New - argNorm: Normalize ARG annotations to ARO
https://argnorm.readthedocs.io/en/latest/whatsnew/#version-070-5-march-2025
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