Luis Pedro Coelho
@luispedrocoelho.bsky.social
Content creator for Elsevier, NPG, and others Microbiome researcher Based in Brisbane
MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...
I would like to do more of these as time goes on. Claude is very good at this (even between when we started drafting the paper and now, the models are so much better!) and I think this can be a great addition to any paper
@bigdatabiology.bsky.social · 3w agoWe updated our companion website to the elusive resistome paper to be more responsive (it's 100% client side now) You can generate all the alternative plots that we could not get into the paper: arg-pipelines.big-data-biology.org
🧬 Want to analyse microbial communities beyond amplicon sequencing? Join Environmental #Metagenomics: From Reads to Genomes (12–16 Oct ) & learn how to process metagenomic data, assemble MAGs & apply modern bioinformatic workflows with Illumina & @nanoporetech.com reads @luispedrocoelho.bsky.social
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
mirdita.org
I've been thinking of how to make tools "AI-ready" so it's not just an empty buzzword I'd like to hear other opinions, but this is what I'm trying with SemiBin: 1) bundle skills with the tool SemiBin2 install-skills will (in the next release) install a skill for claude/codex/...
New newsletter with updates from the group! Focus is on Juan's preprint on the elusive resistome bigdatabiology.substack.com/p/updates-fo...
BDB-Lab June 2026 Updates
The elusive resistome and upcoming travel/conferences
bigdatabiology.substack.com
A bit delayed announcement, but we recently released SemiBin 2.30! No big new features, but it contains a large number of small fixes and improvements (include having had all major LLMs audit and improve the code) bioconda & pypi packages have been updated too github.com/BigDataBiolo...
Release Version 2.3.0 · BigDataBiology/SemiBin
This release bundles a large number of bug fixes (several of which fix silent correctness issues in training and clustering), removes the deprecated SemiBin1 command, and includes many documentatio...
github.com
nintendo’s creation of wario and waluigj was one of the most important advances in manichean religion and philosophy
New #MicrobiomeDigest is OUT microbiomedigest.com/2026/05/29/m... • root microbiome/ @algazuccaro.bsky.social • gut microbiome-epigenetics/ @gangfang.bsky.social • resistome annotation/ @bigdatabiology.bsky.social • invitation for #MVIF 50🎂 / @microbiomevif.bsky.social & more. Happy Friday!
May 29, 2026
See you next week at MVIF! Global microbiome Advancing microbial ecology, microbiomes, and One Health in Africa: From regional initiatives to pan-African flagship programs – Mohamed Hijri – The ISM…
microbiomedigest.com
We started with a simple question: which tool and db should we use for resistome profiling in the EMBARK project? That question sent us down a rabbit hole. Different ARG annotation pipelines don't just give different ARG numbers, they give you different resistome profiles. 1/3
A new substack, following up on last week's arXivgate discussions. The text is not the paper luispedro.substack.com/p/the-text-i...
The text is not the paper
A few notes on authorship in Big Life Sciences
luispedro.substack.com
🧬 Online course - #EnvironmentalMetagenomics this October (12–16 ) with @luispedrocoelho.bsky.social & @oskolkov.bsky.social! Learn state-of-the-art approaches for metagenomic analysis, from read-based profiling to MAG recovery using Illumina + @nanoporetech.com data, SemiBin2, and more.
The preprint is now out: www.biorxiv.org/content/10.6... Thank you to @luispedrocoelho.bsky.social, Juan Inda, and the #SEARCHER_JPIAMR team! Check out the summary thread: bsky.app/profile/bigd... 3/3
@bigdatabiology.bsky.social · 3mo agoHow well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...
I will be in Brazil (São Paulo) for a week for the 55th Annual Meeting of SBBq ! Come say Hi! luispedro.substack.com/p/travel-lin...
Travel. Links. Tweets.
In Brazil next week, venha dizer-me Olá!
luispedro.substack.com
How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...
The elusive resistome: a global comparison reveals large discrepancies among detection pipelines
Identifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174
biorxiv.org
More details to follow later, but this has been in the works for almost 6 years, so it is great to finally see it in preprint form: "The elusive resistome: a global comparison reveals large discrepancies among detection pipelines" www.biorxiv.org/content/10.6...
biorxiv.org
The elusive resistome: a global comparison reveals large discrepancies among detection pipelines https://www.biorxiv.org/content/10.64898/2026.05.11.724158v1
Happiest Birthday @luispedrocoelho.bsky.social!!🎉 #2026 #Birthday #supervisor #memories #Celebrate #BDB @cmrqut.bsky.social #TRI #QUT
Links & Tweets post (plus a picture found on the street) luispedro.substack.com/p/links-twee...
Links. Tweets. Photos (mid-April 2026)
I have created a new section on the substack to contain the Links emails, so you can subscribe/unsubscribe to the Links emails separately from other posts.
luispedro.substack.com
"A lot of what I do with graduate students is what I call unteaching school." A new substack post luispedro.substack.com/p/unteaching...
Unteaching school
A lot of what I do with graduate students is what I call unteaching school.
luispedro.substack.com
BrisJAMS is back this April and it’s shaping up to be a seriously fun night of science, stories, and good vibes 🧪🧫✨ 📅 When: Wednesday, 29 April 2026 | 6:00–7:30pm 📍 Where: The Burrow (Beer Garden Room), West End. 👉 Register via the QR code on the poster!
This simulation-cum-benchmark study on MAG making by @tkorem.bsky.social & team looks really interesting. Loads of plots and results to work through! www.biorxiv.org/content/10.6...
biorxiv.org
Very impressive to see all the diversity hidden and generally missed by common approaches!
Sebastian Schmidt@tsbschm.bsky.social · 4mo agoOur work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com : www.nature.com/articles/s41... See the linked threads for more details!
This, but unironically (especially so in the Age of Claude - taste is that which is scarce)
Oded Rechavi@odedrechavi.bsky.social · 4mo agoEvery PI
Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com : www.nature.com/articles/s41... See the linked threads for more details!
Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology
Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.
nature.com
Sebastian Schmidt@tsbschm.bsky.social · 9mo agoWe'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...
We have always been overwhelmed by the current data explosion! luispedro.substack.com/p/bioinforma...
Bioinformaticians have been writing the same abstract for decades
We have always been overwhelmed by the data explosion
luispedro.substack.com
We have always been overwhelmed by the current data explosion! luispedro.substack.com/p/bioinforma...
Bioinformaticians have been writing the same abstract for decades
We have always been overwhelmed by the data explosion
luispedro.substack.com
Monthly median Received to Accepted time (days) at Nature Genetics
