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
Strobealign v0.17.0 is out! github.com/ksahlin/stro...
Release Version 0.17.0 · ksahlin/strobealign
Changes
#504: Introduce collinear chaining as the new default mapping and alignment method, replacing NAMs. This reproduces the Minimap2 chaining algorithm providing better mapping accuracy. NAMs ...
github.com
December 29, 2025 at 5:50 AM
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...
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...
Links. Photos. (December 2025)
Missing my publishing goal for 2025...
luispedro.substack.com
December 21, 2025 at 7:44 AM
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...
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...
Reposted by Luis Pedro Coelho
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'.
December 13, 2025 at 12:53 PM
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
The winning streak for the shingles vaccine continues...I'm starting to get optimistic on this one 🤞🙏:
jenndowd.substack.com/p/more-good-... #episky #medsky #idsky #econsky #publichealth #dementia
jenndowd.substack.com/p/more-good-... #episky #medsky #idsky #econsky #publichealth #dementia
More Good News on the Shingles Vaccine and Dementia
Two new studies add more evidence of a protective effect
jenndowd.substack.com
December 10, 2025 at 9:45 PM
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
Reposted by Luis Pedro Coelho
"there's a new serif in town"
Marco Rubio ordered diplomats to return to using Times New Roman font in official communications, calling his predecessor's decision to adopt Calibri a “wasteful” diversity move
Rubio Stages Font Coup: Times New Roman Ousts Calibri
The secretary of state called it a "wasteful" diversity move, according to an internal department cable seen by Reuters.
www.huffpost.com
December 10, 2025 at 1:06 AM
"there's a new serif in town"
Reposted by Luis Pedro Coelho
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
December 3, 2025 at 10:26 AM
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
Reposted by Luis Pedro Coelho
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
one of the reasons that the STEM-humanitiies culture war is stupid is that there's a lot of interesting stuff there at the intersection of the two. like it's very sociologically interesting the way that programming languages are maintained, propagated, and evolve.
December 2, 2025 at 9:49 PM
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
Reposted by Luis Pedro Coelho
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
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
December 2, 2025 at 5:52 PM
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
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
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