Luis Pedro Coelho
@luispedrocoelho.bsky.social
Content creator for Elsevier, NPG, and others
Microbiome researcher
Based in Brisbane
Microbiome researcher
Based in Brisbane
Reposted by Luis Pedro Coelho
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...
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...
GitHub - BigDataBiology/macrel: Predict AMPs in (meta)genomes and peptides
Predict AMPs in (meta)genomes and peptides. Contribute to BigDataBiology/macrel development by creating an account on GitHub.
github.com
November 25, 2025 at 5:05 AM
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...
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...
Reposted by Luis Pedro Coelho
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
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
bsky.app
November 23, 2025 at 10:59 PM
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
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
Reposted by Luis Pedro Coelho
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: academic.oup.com/nar/article/...
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob
academic.oup.com
November 20, 2025 at 8:50 AM
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: academic.oup.com/nar/article/...
Reposted by Luis Pedro Coelho
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
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob
dx.doi.org
November 20, 2025 at 9:20 AM
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
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
November 21, 2025 at 12:46 AM
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
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
Reposted by Luis Pedro Coelho
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...
www.biorxiv.org/content/10.1...
Hidden but discoverable diversity in the global microbiome
Cataloguing Earth's biodiversity remains one of the most formidable challenges in biology, and the greatest diversity is expected to reside among the smallest organisms: microbes. Yet the ongoing cens...
www.biorxiv.org
November 18, 2025 at 8:53 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Luis Pedro Coelho
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!
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!
October 17, 2025 at 7:33 AM
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!
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!
Reposted by Luis Pedro Coelho
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...
@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
September 23, 2025 at 11:24 AM
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...
@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...
Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases
doi.org/10.1101/2025...
September 18, 2025 at 12:01 PM
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...
Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases
doi.org/10.1101/2025...
Reposted by Luis Pedro Coelho
🦠🌍 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!
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!
September 17, 2025 at 7:52 AM
🦠🌍 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!
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!
Reposted by Luis Pedro Coelho
#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
#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
September 3, 2025 at 3:14 PM
#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
#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...
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...
August 22, 2025 at 4:35 PM
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...
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...
Reposted by Luis Pedro Coelho
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
💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰
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
💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰
August 5, 2025 at 6:55 AM
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
💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰
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
💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰
Reposted by 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
- 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
July 31, 2025 at 8:25 PM
- 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
- 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
ISMB 2025 Schedule
Interactive schedule for the ISMB 2025 conference
ismb-schedule.luispedro.org
July 23, 2025 at 1:17 PM
New feature this year, share a talk link
July 22, 2025 at 9:52 AM
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
ismb-schedule.luispedro.org
Main
ismb-schedule.luispedro.org
July 21, 2025 at 1:33 PM
After a few people asked me about it, I gave in and updated my light ISMB schedule website for #ISMBECCB2025
ismb-schedule.luispedro.org
ismb-schedule.luispedro.org
UK. Links. Tweets. Photo
Visiting the UK. Links. Photo
luispedro.substack.com
July 13, 2025 at 11:41 AM
Reposted by Luis Pedro Coelho
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!
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
July 4, 2025 at 4:34 AM
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!
Check it out and share widely: www.abacbs.org/abacbs2025
Registrations and abstract submissions open next week, with abstracts due in August!
Reposted by Luis Pedro Coelho
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
We predict that there are 10 archaeal and 145 bacterial novel phyla across all habitats.
#MicrobialDarkMatter #TreeOfLife #Microbiome #Archaea #Bacteria #Metagenomics
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 🧵.
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 🧵.
A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
June 30, 2025 at 2:50 PM
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
We predict that there are 10 archaeal and 145 bacterial novel phyla across all habitats.
#MicrobialDarkMatter #TreeOfLife #Microbiome #Archaea #Bacteria #Metagenomics
Reposted by Luis Pedro Coelho
A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
June 27, 2025 at 2:18 PM
A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
Reposted by Luis Pedro Coelho
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 🧵.
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 🧵.
A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
June 27, 2025 at 8:10 PM
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 🧵.
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 🧵.
Reposted by Luis Pedro Coelho
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?"
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?"
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 🧵.
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 🧵.
A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
June 27, 2025 at 8:18 PM
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?"
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?"
Reposted by Luis Pedro Coelho
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
And of course to the lead authors @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social
June 27, 2025 at 8:10 PM
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
And of course to the lead authors @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social